That a John lived a long life in Asia (until the time of Trajan) is reported by Irenaeus and others, and those testimonies are fairly well known:
Irenaeus, Against Heresies 3.3.4: 4 .... There is also a very powerful Epistle of Polycarp written to the Philippians, from which those who choose to do so, and are anxious about their salvation, can learn the character of his faith, and the preaching of the truth. Then, again, the Church in Ephesus, founded by Paul, and having John remaining among them permanently until the times of Trajan [Ἰωάννου δὲ παραμείναντος αὐτοῖς μέχρι τῶν Τραϊανοῦ χρόνων], is a true witness of the tradition of the apostles.
Acts of John 115: 115 And having sealed himself in every part, he stood and said, "You are with me, O Lord Jesus Christ," and laid himself down in the trench where he had strown his garments; and, having said unto us, "Peace be with you, brethren," he gave up his spirit rejoicing. / 115 Καὶ σφραγισάμενος ἑαυτὸν ὅλον ἑστὼς καὶ εἰρηκὼς· «Σὺ μετ' ἐμοῦ κύριε Ἰησοῦ Χριστέ,» κατεκλίθη ἐν τῷ σκάμματι ἔνθα τὰ ἱμάτια αὐτοῦ ὑπέστρωσεν· καὶ εἰπὼν ἡμῖν· «Εἰρήνη μεθ' ὑμῶν, ἀδελφοί,» παρέδωκε τὸ πνεῦμα χαίρων.
M. R. James, The Apocryphal New Testament, page 270: The less good Greek manuscripts and some versions are not content with this simple ending. The Latin says that after the prayer a great light appeared over the apostle for the space of an hour, so bright that no one could look at it. (Then he laid himself down and gave up the ghost.) We who were there rejoiced, some of us, and some mourned.... And forthwith manna issuing from the tomb was seen of all, which manna that place produceth even unto this day...." But perhaps the best conclusion is that of one Greek manuscript: "We brought a linen cloth and spread it upon him, and went into the city. And on the day following we went forth and found not his body, for it was translated by the power of our Lord Jesus Christ, unto whom be glory...." Another says: "On the morrow we dug in the place, and him we found not, but only his sandals, and the earth moving..., and after that we remembered that which was spoken by the Lord unto Peter...." Augustine (On John xxi) reports the belief that in his time the earth over the grave was seen to move as if stirred by John's breathing.
Eusebius, History of the Church 3.31.2-3: 2 The time of John's death has also been given in a general way, but his burial place is indicated by an epistle of Polycrates (who was bishop of the parish of Ephesus), addressed to Victor, bishop of Rome. In this epistle he mentions him together with the apostle Philip and his daughters in the following words: 3 "For in Asia also great lights have fallen asleep, which shall rise again on the last day, at the coming of the Lord, when he shall come with glory from heaven and shall seek out all the saints. Among these are Philip, one of the twelve apostles, who sleeps in Hierapolis, and his two aged virgin daughters, and another daughter who lived in the Holy Spirit and now rests at Ephesus; and moreover John, who was both a witness and a teacher, who reclined upon the bosom of the Lord, and being a priest wore the sacerdotal plate. He also sleeps at Ephesus." So much concerning their death. / 2 Τοῦ δὲ Ἰωάννου τὰ μὲν τοῦ χρόνου ἤδη πως εἴρηται, τὸ δέ γε τοῦ σκηνώματος αὐτοῦ χωρίον ἐξ ἐπιστολῆς Πολυκράτους τῆς δ' ἐν Ἐφέσῳ παροικίας ἐπίσκοπος οὗτος ἦν ἐπιδείκνυται, ἣν Οὐίκτορι Ῥωμαίων ἐπισκόπῳ γράφων, ὁμοῦ τε αὐτοῦ καὶ Φιλίππου μνημονεύει τοῦ ἀποστόλου τῶν τε τούτου θυγατέρων ὧδέ πως· 3 «Καὶ γὰρ κατὰ τὴν Ἀσίαν μεγάλα στοιχεῖα κεκοίμηται· ἅτινα ἀναστήσεται τῇ ἐσχάτῃ ἡμέρᾳ τῆς παρουσίας τοῦ κυρίου, ἐν ᾗ ἔρχεται μετὰ δόξης ἐξ οὐρανοῦ καὶ ἀναζητήσει πάντας τοὺς ἁγίους, Φίλιππον τῶν δώδεκα ἀποστόλων, ὃς κεκοίμηται ἐν Ἱεραπόλει καὶ δύο θυγατέρες αὐτοῦ γεγηρακυῖαι παρθένοι καὶ ἡ ἑτέρα αὐτοῦ θυγάτηρ ἐν ἁγίῳ πνεύματι πολιτευσαμένη ἐν Ἐφέσῳ ἀναπαύεται· ἔτι δὲ καὶ Ἰωάννης, ὁ ἐπὶ τὸ στῆθος τοῦ κυρίου ἀναπεσών, ὃς ἐγενήθη ἱερεὺς τὸ πέταλον πεφορεκὼς καὶ μάρτυς καὶ διδάσκαλος, οὗτος ἐν Ἐφέσῳ κεκοίμηται.» Ταῦτα καὶ περὶ τῆς τῶνδε τελευτῆς.
Eusebius, History of the Church 5.24.1-8: 1 But the bishops of Asia, led by Polycrates, decided to hold to the old custom handed down to them. He himself, in a letter which he addressed to Victor and the church of Rome, set forth in the following words the tradition which had come down to him: 2 "We observe the exact day; neither adding, nor taking away. For in Asia also great lights have fallen asleep, which shall rise again on the day of the Lord's coming, when he shall come with glory from heaven, and shall seek out all the saints. Among these are Philip, one of the twelve apostles, who fell asleep in Hierapolis; and his two aged virgin daughters, and another daughter, who lived in the Holy Spirit and now rests at Ephesus; and, moreover, John, who was both a witness and a teacher, who reclined upon the bosom of the Lord, and, being a priest, wore the sacerdotal plate. 3 He fell asleep at Ephesus. 4 And Polycarp in Smyrna, who was a bishop and martyr; and Thraseas, bishop and martyr from Eumenia, who fell asleep in Smyrna. 5 Why need I mention the bishop and martyr Sagaris who fell asleep in Laodicea, or the blessed Papirius, or Melito, the Eunuch who lived altogether in the Holy Spirit, and who lies in Sardis, awaiting the episcopate from heaven, when he shall rise from the dead? 6 All these observed the fourteenth day of the passover according to the Gospel, deviating in no respect, but following the rule of faith. And I also, Polycrates, the least of you all, do according to the tradition of my relatives, some of whom I have closely followed. For seven of my relatives were bishops; and I am the eighth. And my relatives always observed the day when the people put away the leaven. 7 I, therefore, brethren, who have lived sixty-five years in the Lord, and have met with the brethren throughout the world, and have gone through every Holy Scripture, am not affrighted by terrifying words. For those greater than I have said, 'We ought to obey God rather than man' (= Acts 5.29)." 8 He then writes of all the bishops who were present with him and thought as he did. His words are as follows: "I could mention the bishops who were present, whom I summoned at your desire; whose names, should I write them, would constitute a great multitude. And they, beholding my littleness, gave their consent to the letter, knowing that I did not bear my gray hairs in vain, but had always governed my life by the Lord Jesus." / 1 Τῶν δὲ ἐπὶ τῆς Ἀσίας ἐπισκόπων τὸ πάλαι πρότερον αὐτοῖς παραδοθὲν διαφυλάττειν ἔθος χρῆναι διισχυριζομένων ἡγεῖτο Πολυκράτης· ὃς καὶ αὐτὸς ἐν ᾗ πρὸς Βίκτορα καὶ τὴν Ῥωμαίων ἐκκλησίαν διετυπώσατο γραφῇ τὴν εἰς αὐτὸν ἐλθοῦσαν παράδοσιν ἐκτίθεται διὰ τούτων· 2 «Ἡμεῖς οὖν ἀρᾳδιούργητον ἄγομεν τὴν ἡμέραν, μήτε προστιθέντες μήτε ἀφαιρούμενοι. Καὶ γὰρ κατὰ τὴν Ἀσίαν μεγάλα στοιχεῖα κεκοίμηται· ἅτινα ἀναστήσεται τῇ ἡμέρᾳ τῆς παρουσίας τοῦ κυρίου, ἐν ᾗ ἔρχεται μετὰ δόξης ἐξ οὐρανῶν καὶ ἀναζητήσει πάντας τοὺς ἁγίους, Φίλιππον τῶν δώδεκα ἀποστόλων, ὃς κεκοίμηται ἐν Ἱεραπόλει καὶ δύο θυγατέρες αὐτοῦ γεγηρακυῖαι παρθένοι καὶ ἡ ἑτέρα αὐτοῦ θυγάτηρ ἐν ἁγίῳ πνεύματι πολιτευσαμένη ἐν Ἐφέσῳ ἀναπαύεται· 3 ἔτι δὲ καὶ Ἰωάννης ὁ ἐπὶ τὸ στῆθος τοῦ κυρίου ἀναπεσών, ὃς ἐγενήθη ἱερεὺς τὸ πέταλον πεφορεκὼς καὶ μάρτυς καὶ διδάσκαλος· οὗτος ἐν Ἐφέσῳ κεκοίμηται, 4 ἔτι δὲ καὶ Πολύκαρπος ἐν Σμύρνῃ, καὶ ἐπίσκοπος καὶ μάρτυς· καὶ Θρασέας, καὶ ἐπίσκοπος καὶ μάρτυς ἀπὸ Εὐμενείας, ὃς ἐν Σμύρνῃ κεκοίμηται. 5 Τί δὲ δεῖ λέγειν Σάγαριν ἐπίσκοπον καὶ μάρτυρα, ὃς ἐν Λαοδικείᾳ κεκοίμηται, ἔτι δὲ καὶ Παπίριον τὸν μακάριον καὶ Μελίτωνα τὸν εὐνοῦχον, τὸν ἐν ἁγίῳ πνεύματι πάντα πολιτευσάμενον, ὃς κεῖται ἐν Σάρδεσιν περιμένων τὴν ἀπὸ τῶν οὐρανῶν ἐπισκοπὴν ἐν ᾗ ἐκ νεκρῶν ἀναστήσεται; 6 Οὗτοι πάντες ἐτήρησαν τὴν ἡμέραν τῆς τεσσαρεσκαιδεκάτης τοῦ πάσχα κατὰ τὸ εὐαγγέλιον, μηδὲν παρεκβαίνοντες, ἀλλὰ κατὰ τὸν κανόνα τῆς πίστεως ἀκολουθοῦντες· «Ἔτι δὲ κἀγὼ ὁ μικρότερος πάντων ὑμῶν Πολυκράτης, κατὰ παράδοσιν τῶν συγγενῶν μου, οἷς καὶ παρηκολούθησά τισιν αὐτῶν. Ἑπτὰ μὲν ἦσαν συγγενεῖς μου ἐπίσκοποι, ἐγὼ δὲ ὄγδοος· καὶ πάντοτε τὴν ἡμέραν ἤγαγον οἱ συγγενεῖς μου ὅταν ὁ λαὸς ἤρνυεν τὴν ζύμην. 7 Ἐγὼ οὖν, ἀδελφοί, ἑξήκοντα πέντε ἔτη ἔχων ἐν κυρίῳ καὶ συμβεβληκὼς τοῖς ἀπὸ τῆς οἰκουμένης ἀδελφοῖς καὶ πᾶσαν ἁγίαν γραφὴν διεληλυθώς, οὐ πτύρομαι ἐπὶ τοῖς καταπλησσομένοις· οἱ γὰρ ἐμοῦ μείζονες εἰρήκασι « Πειθαρχεῖν δεῖ θεῷ μᾶλλον ἢ ἀνθρώποις.» 8 Τούτοις ἐπιφέρει περὶ τῶν γράφοντι συμπαρόντων αὐτῷ καὶ ὁμοδοξούντων ἐπισκόπων ταῦτα λέγων· «Ἐδυνάμην δὲ τῶν ἐπισκόπων τῶν συμπαρόντων μνημονεῦσαι, οὓς ὑμεῖς ἠξιώσατε μετακληθῆναι ὑπ´ ἐμοῦ καὶ μετεκαλεσάμην· ὧν τὰ ὀνόματα ἐὰν γράφω, πολλὰ πλήθη εἰσίν· οἳ δὲ εἰδότες τὸν μικρόν μου ἄνθρωπον συνηυδόκησαν τῇ ἐπιστολῇ, εἰδότες ὅτι εἰκῇ πολιὰς οὐκ ἤνεγκα, ἀλλ´ ἐν Χριστῷ Ἰησοῦ πάντοτε πεπολίτευμαι.»
There is also the suggestion (mentioned by MacDonald) that James and John were called the Sons of Thunder precisely because James died young (as represented by the mortal Castor, son of Zeus) while the other lived a very long life (as represented by the immortal Pollux, son of Zeus).
But what about the other important passage in the gospel of Mark?
Did Mark report John's martyrdom while John was still alive? I tend to doubt it. Rather, Mark "knew" that both of the sons of Zebedee had died as martyrs. Other sources agree that John died a martyr.
First, there is possibly one (negative) argument to be made from silence. Heracleon, as quoted by Clement of Alexandria in Miscellanies 4.9, writes that "Matthew, Philip, Thomas, Levis, and many others" (Ματθαῖος, Φίλιππος, Θωμᾶς, Λευῒς καὶ ἄλλοι πολλοί) have made "the confession through the voice" (τὴν διὰ τῆς φωνῆς ὁμολογίαν) — that is, they died in ordinary ways rather than as martyrs. That as prominent a disciple as John of Zebedee is not listed in this context may indicate knowledge of his martyrdom.
As for other (positive) arguments, there are the martyrologies:
Vincent Henry Stanton, The Gospels as Historical Documents, page 115: In the Armenian Calendar the entry for Dec. 28 (the festivals of the Sons of Zebedee and of Peter and Paul have here been inverted) is "The festival of the holy sons of thunder, James and John."
Hieronymian Calendar, December 27 (apud Vincent Henry Stanton, page 115): Adsumptio S. Johannis Evangelistae apud Ephesum et ordinatio episcopatus S. Jacobi fratris Domini qui ab apostolis primus ex Judaeis Hierosolymis episcopus est ordinatus. / Assumption of Saint John the Evangelist at Ephesus and the ordination of the episcopate of Saint James/Jacob the brother of the Lord who was the first bishop ordained from among the apostles from the Jews of Jerusalem.
Robert Eisler, The Enigma of the Fourth Gospel, page 62: The famous Missal of Bobbio reflecting the pre-Carolingian ritual of the Church of Paris — where Syrians had occupied not only the bishop's seat, but all the most influential ecclesiastical offices under the Merovingian kings — offers, after the mass for Christmas Day (No. 6), as No. 7 the mass for St. Stephen, as No. 8 the mass in memory of the massacre of the Innocent Children, and as No. 9 Missa Jacobi el Johannis. The gospel lessons for the day are Matt. xx. 20-23: accessit mater filiorum Zebedaei... containing Jesus' prophecy of the martyrdom of the two brothers, followed by Acts xii. 1-3: Misit Herodes rex manus ut affligeret quosdam de ecclesia... the account of how this prophecy was fulfilled in the case of St. James.
Martyrology of Carmona, December 27 & June 24 (apud Eisler, page 61): VI K(alendas Io)annis apostole XII. .... VIII Kal(endas) Julias S(an)c(ti) Joanni(s) B(aptistae).
Carthaginian Calendar, December 27: VI. Kal. Jan. sancti Johannis Baptistae, et Jacobi Apostoli, quem Herodes occidit. / December 27, of Saint John the Baptist and James/Jacob the Apostle, whom Herod murdered. [Link. That John the Baptist is a mistake for John of Zebedee in the Carthaginian Calendar is supported by the presence of John the Baptist's usual feast day elsewhere on this same calendar.]
Carthaginian Calendar, June 24: VIII. Kal. Jul. sancti Johannis Baptistae.... / June 24, of Saint John the Baptist....
Eusebius, History of the Church 2.9.1-4: 1 "Now about that time" — it is clear that he means the time of Claudius — "Herod the King stretched forth his hands to vex certain of the Church. And he killed James the brother of John with the sword" (= Acts 12.1-2). 2 And concerning this James, Clement, in the seventh book of his Hypotyposes, relates a story which is worthy of mention, telling it as he received it from those who had lived before him. He says that the one who led James to the judgment seat, when he saw him bearing his testimony, was moved, and confessed that he was himself also a Christian. 3 They were both therefore, he says, led away together; and on the way he begged James to forgive him. And he, after considering a little, said, "Peace be with you," and kissed him. And thus they were both beheaded at the same time. 4 And then, as the divine Scripture says (= Acts 12.3-17), Herod, upon the death of James, seeing that the deed pleased the Jews, attacked Peter also and committed him to prison, and would have slain him if he had not, by the divine appearance of an angel who came to him by night, been wonderfully released from his bonds, and thus liberated for the service of the Gospel. Such was the providence of God in respect to Peter. / 1 «Κατ´ ἐκεῖνον δὲ τὸν καιρόν,» δῆλον δ´ ὅτι τὸν ἐπὶ Κλαυδίου, «ἐπέβαλεν Ἡρῴδης ὁ βασιλεὺς τὰς χεῖρας κακῶσαί τινας τῶν ἀπὸ τῆς ἐκκλησίας, ἀνεῖλεν δὲ Ἰάκωβον τὸν ἀδελφὸν Ἰωάννου μαχαίρᾳ.» <2> περὶ τούτου δ´ ὁ Κλήμης τοῦ Ἰακώβου καὶ ἱστορίαν μνήμης ἀξίαν ἐν τῇ τῶν Ὑποτυπώσεων ἑβδόμῃ παρατίθεται ὡς ἂν ἐκ παραδόσεως τῶν πρὸ αὐτοῦ, φάσκων ὅτι δὴ ὁ εἰσαγαγὼν αὐτὸν εἰς δικαστήριον, μαρτυρήσαντα αὐτὸν ἰδὼν κινηθείς, ὡμολόγησεν εἶναι καὶ αὐτὸς ἑαυτὸν Χριστιανόν. <3> «Συναπήχθησαν οὖν ἄμφω,» φησίν, «καὶ κατὰ τὴν ὁδὸν ἠξίωσεν ἀφεθῆναι αὐτῷ ὑπὸ τοῦ Ἰακώβου· ὁ δὲ ὀλίγον σκεψάμενος, εἰρήνη σοι, εἶπεν καὶ κατεφίλησεν αὐτόν. Καὶ οὕτως ἀμφό τεροι ὁμοῦ ἐκαρατομήθησαν.» <4> τότε δῆτα, ὥς φησιν ἡ θεία γραφή, ἰδὼν Ἡρῴδης ἐπὶ τῇ τοῦ Ἰακώβου ἀναιρέσει πρὸς ἡδονῆς γεγονὸς τὸ πραχθὲν τοῖς Ἰουδαίοις, ἐπιτίθεται καὶ Πέτρῳ, δεσμοῖς τε αὐτὸν παραδούς, ὅσον οὔπω καὶ τὸν κατ´ αὐτοῦ φόνον ἐνήργησεν ἄν, εἰ μὴ διὰ θείας ἐπιφανείας, ἐπιστάντος αὐτῷ νύκτωρ ἀγγέλου, παραδό ξως τῶν εἱργμῶν ἀπαλλαγείς, ἐπὶ τὴν τοῦ κηρύγματος ἀφεῖται διακονίαν. Καὶ τὰ μὲν κατὰ Πέτρον οὕτως εἶχεν οἰκονομίας. [Could this legend have originally been a way to explain the presence of another man (= John!) killed alongside James?]
And is it possible that the beheading of John the baptist by Herod Antipas may actually be a garbled transmission of the death of John of Zebedee by beheading (along with and like his brother James) by Herod Agrippa? John the baptist's entire death in Matthew 14.1-12 = Mark 6.14-29 (= Luke 9.7-9) seems to me to be based on the beheading of Vashti in Jewish midrash.
As for the two tombs in Ephesus, they may have both been for the same John:
And of course there is this late report about Papias:
Or did Philip misread Origen and then attribute it to Papias by mistake?
This suggestion has been made, but I am not sure.
At any rate, some sources say that John lived a long life before dying (among which some of these former even assert that he died peacefully), while others say that he died a martyr, like his brother James, and apparently, according to some of these latter, on the same day (as suggested by the feast days).
This is certainly possible. Both are associated with Asia.
I suspect that the Johannine epistles were written by the Elder John mentioned by Papias. This would explain their titles (as epistles "of John") and the internal authorship claim of 2 and 3 John as having been written by someone who could be referred to simply as "the Elder."...(and that they could also be the pillar John), but even if they aren't, do you think either of them could have a) written all or some of the Johannine epistles; and b) that these epistles and/or the fame of either of these Johns could have inspired the author of the gospel of John to pretend be one of them (and/or could have inspired whoever called that gospel John)?
I think that the gospel of John came later, and in multiple layers. (Evidence for this gospel being layered is abundant.) Whoever added the appendix (= John 21) also added the beloved disciple to a gospel which previously lacked him. This beloved disciple may well have been intended to be the Elder John, since we find the author of the gospel of John correcting or critiquing Matthew and Mark quite a lot; I suggest that the editors (lurking behind the plural "we") were following John the Elder's lead, who, according to Papias, was not above correcting or critiquing the gospels of Matthew and Mark.
Before the beloved disciple was added to the text, the most beloved individual in the gospel was Lazarus. Calling this upstart disciple "beloved" was a way of replacing Lazarus with the beloved disciple, so far as intimacy with Jesus is concerned.
Even if John the Elder is the beloved disciple (and I may be wrong about that), I doubt he was ever a follower of Jesus. He may have met Jesus, or someone he thought was Jesus, as a very young man, or even as a child, in Palestine, thus explaining this weird tradition:
Because so precious little is said about John the Pillar, I am not sure which other John he may or may not be; nor am I sure where he may fit in.
YMMV.