Ellicott's Commentary for English Readers:
Which is in heaven.—These words are omitted in some MSS., including the Sinaitic and the Vatican. The judgment of most modern editors (not including Westcott and Hort) retains them. It is an instance where it is hard to account for the insertion by a copyist, but where the omission is not unlikely, owing to their seeming difficulty. And yet the difficulty is one which vanishes before the true idea of heaven. If heaven is thought of as a place infinitely distant beyond clouds and sky, or as a time in the far future when this world’s life shall end, then it is indeed hard to understand what is here meant by “the Son of Man which is in heaven;” and a copyist may well have found in omission the easiest solution of the difficulty. But if heaven is something wholly different from this coldness of distance in space or time; if it is a state, a life, in which we are, which is in us—now in part, hereafter in its fulness—then may we understand and with glad hearts hold to the vital truth that the Son of Man, who came down from heaven, was ever in heaven; and that every son of man who is born of water and of the Spirit is “made a member of Christ, a child of God, and an inheritor (in the present, κληρονόμος) of the kingdom of heaven.”
Cambridge Bible for Schools and Colleges:
which is in heaven] These words are omitted in the best MSS. If they are retained, the meaning is ‘Whose proper home is heaven.’ Or the Greek participle may be the imperfect tense (comp. John 6:62, John 9:25, John 17:5), which was in heaven before the Incarnation. It is doubtful whether in this verse we have any direct allusion to the Ascension, though this is sometimes assumed.
NET Bible Footnote:
tc Most witnesses, including a few important ones (A[*] Θ Ψ 050 Ë1,13 Ï latt syc,p,h), have at the end of this verse “the one who is in heaven” (ὁ ὢν ἐν τῷ οὐρανῷ, Jo wn en tw ouranw). A few others have variations on this phrase, such as “who was in heaven” (e syc), or “the one who is from heaven” (0141 pc sys). The witnesses normally considered the best, along with several others, lack the phrase in its entirety (Ì66,75 א B L T Ws 083 086 33 1241 pc co). On the one hand, if the reading ὁ ὢν ἐν τῷ οὐρανῷ is authentic it may suggest that while Jesus was speaking to Nicodemus he spoke of himself as in heaven even while he was on earth. If that is the case, one could see why variations from this hard saying arose: “who was in heaven,” “the one who is from heaven,” and omission of the clause. At the same time, such a saying could be interpreted (though with difficulty) as part of the narrator’s comments rather than Jesus’ statement to Nicodemus, alleviating the problem. And if v. 13 was viewed in early times as the evangelist’s statement, “the one who is in heaven” could have crept into the text through a marginal note. Other internal evidence suggests that this saying may be authentic. The adjectival participle, ὁ ὤν, is used in the Fourth Gospel more than any other NT book (though the Apocalypse comes in a close second), and frequently with reference to Jesus (1:18; 6:46; 8:47). It may be looking back to the LXX of Exod 3:14 (ἐγώ εἰμι ὁ ὤν). Especially since this exact construction is not necessary to communicate the location of the Son of Man, its presence in many witnesses here may suggest authenticity. Further, John uses the singular of οὐρανός (ourano", “heaven”) in all 18 instances of the word in this Gospel, and all but twice with the article (only 1:32 and 6:58 are anarthrous, and even in the latter there is significant testimony to the article). At the same time, the witnesses that lack this clause are very weighty and must not be discounted. Generally speaking, if other factors are equal, the reading of such mss should be preferred. And internally, it could be argued that ὁ ὤν is the most concise way to speak of the Son of Man in heaven at that time (without the participle the point would be more ambiguous). Further, the articular singular οὐρανός is already used twice in this verse, thus sufficiently prompting scribes to add the same in the longer reading. This combination of factors suggests that ὁ ὢν ἐν τῷ οὐρανῷ is not a genuine Johannism. Further intrinsic evidence against the longer reading relates to the evangelist’s purposes: If he intended v. 13 to be his own comments rather than Jesus’ statement, his switch back to Jesus’ words in v. 14 (for the lifting up of the Son of Man is still seen as in the future) seems inexplicable. The reading “who is in heaven” thus seems to be too hard. All things considered, as intriguing as the longer reading is, it seems almost surely to have been a marginal gloss added inadvertently to the text in the process of transmission. For an argument in favor of the longer reading, see David Alan Black, “The Text of John 3:13,” GTJ 6 (1985): 49-66.
Robertson's Word Pictures in the New Testament:
Which is in heaven (ο ων εν τωι ουρανωι — ho ōn en tōi ouranōi). This phrase is added by some manuscripts, not by Aleph B L W 33, and, if genuine, would merely emphasize the timeless existence of God‘s Son who is in heaven even while on earth. Probably a gloss. But “the Son of man” is genuine. He is the one who has come down out of heaven.
Peter Pett's Commentary on the Bible:
‘Who is in Heaven’. This is omitted in many manuscripts, and although it is fairly strongly evidenced the weight of evidence must be seen as against it (p66, Aleph, B, L, W omit it. A Theta f1 f13 include it). However, the idea behind it, that Jesus has access to Heaven’s secrets is unquestionable (Matthew 11:25-27).
καὶ οὐδεὶς ἀναβέβηκεν εἰς τὸν οὐρανὸν εἰ μὴ ὁ ἐκ τοῦ οὐρανοῦ καταβάς, ὁ υἱὸς τοῦ ἀνθρώπου.