John 20:27-29
27 Then saith he to Thomas, Reach hither thy finger, and behold my hands; and reach hither thy hand, and thrust it into my side: and be not faithless, but believing.
28 And Thomas answered and said unto him, My Lord and my God.
29 Jesus saith unto him, Thomas, because thou hast seen me, thou hast believed: blessed are they that have not seen, and yet have believed.
Thomas calls Jesus "my Lord and my God", and Jesus commends him for believing.
While Thomas's confession could be calling Jesus Himself God in the secondary or non-absolute sense as described in John 10:33-36, it is more likely referring to Thomas confessing that Jesus is the manifestation of the Father to them ("My Lord [Jesus], and my God [the manifestation of the God that I worship]"), as Jesus had told His disciples earlier in John's Gospel - and Thomas is specifically named in the scene - "he that has seen me has seen the Father":
John 14:4-11
4 And whither I go ye know, and the way ye know.
5 Thomas saith unto him, Lord, we know not whither thou goest; and how can we know the way?
6 Jesus saith unto him, I am the way, the truth, and the life: no man cometh unto the Father, but by me.
7 If ye had known me, ye should have known my Father also: and from henceforth ye know him, and have seen him.
8 Philip saith unto him, Lord, shew us the Father, and it sufficeth us.
9 Jesus saith unto him, Have I been so long time with you, and yet hast thou not known me, Philip? he that hath seen me hath seen the Father; and how sayest thou then, Shew us the Father?
10 Believest thou not that I am in the Father, and the Father in me? the words that I speak unto you I speak not of myself: but the Father that dwelleth in me, he doeth the works.
11 Believe me that I am in the Father, and the Father in me: or else believe me for the very works' sake.
The theme of seeing the Father in Jesus is spread throughout the Gospel of John, which says in chapter 1, "No man has seen God at any time; the only begotten Son, which is in the bosom of the Father, he has declared him" (John 1:18), and later has Jesus saying, "he that sees me sees Him that sent me" (John 12:45). Ultimately, this theme culminates in John chapter 20, in the passage in question.
Additionally, Jesus, in the same chapter as the passage in question, places God above Himself (John 20:17), and elsewhere states that the Father is "the only true God" (John 17:3). The Gospel of John, considered in its totality, is not confusing or ambiguous on this point.