in our book "Insight on the Scriptures" there is an explanation of this or rather several possible explanations. What did Thomas mean when he said to Jesus, “My Lord and my God”?
"On the occasion of Jesus’ appearance to Thomas and the other apostles, which had removed Thomas’ doubts of Jesus’ resurrection, the now-convinced Thomas exclaimed to Jesus: “My Lord and my God! [literally, “The Lord of me and the God (ho The·os′) of me!”].” (Joh 20:24-29) Some scholars have viewed this expression as an exclamation of astonishment spoken to Jesus but actually directed to God, his Father. However, others claim the original Greek requires that the words be viewed as being directed to Jesus. Even if this is so, the expression “My Lord and my God” would still have to harmonize with the rest of the inspired Scriptures. Since the record shows that Jesus had previously sent his disciples the message, “I am ascending to my Father and your Father and to my God and your God,” there is no reason for believing that Thomas thought Jesus was the Almighty God. (Joh 20:17) John himself, after recounting Thomas’ encounter with the resurrected Jesus, says of this and similar accounts: “But these have been written down that you may believe that Jesus is the Christ the Son of God, and that, because of believing, you may have life by means of his name.”—Joh 20:30, 31.
"So, Thomas may have addressed Jesus as “my God” in the sense of Jesus’ being “a god” though not the Almighty God, not “the only true God,” to whom Thomas had often heard Jesus pray. (Joh 17:1-3) Or he may have addressed Jesus as “my God” in a way similar to expressions made by his forefathers, recorded in the Hebrew Scriptures, with which Thomas was familiar. On various occasions when individuals were visited or addressed by an angelic messenger of Jehovah, the individuals, or at times the Bible writer setting out the account, responded to or spoke of that angelic messenger as though he were Jehovah God. (Compare Ge 16:7-11, 13; 18:1-5, 22-33; 32:24-30; Jg 6:11-15; 13:20-22.) This was because the angelic messenger was acting for Jehovah as his representative, speaking in his name, perhaps using the first person singular pronoun, and even saying, “I am the true God.” (Ge 31:11-13; Jg 2:1-5) Thomas may therefore have spoken to Jesus as “my God” in this sense, acknowledging or confessing Jesus as the representative and spokesman of the true God. Whatever the case, it is certain that Thomas’ words do not contradict the clear statement he himself had heard Jesus make, namely, “The Father is greater than I am.”—Joh 14:28."
Me again. I particularly like the last part of this explanation because it IS true that certain angelic visitors were addressed as "Jehovah". In Genesis, Abraham is visited by 3 angels that tell him that Sodom and Gomorrah are going to be destroyed. Abraham is concerned about his nephew Lot who lives in that region and he pleads with "Jehovah". Obviously the Bible in other places tells us that "no one has seen God at any time", and Jehovah himself told Moses that no one could see his face and yet live.
Two of the Angels leave Abraham and go toward the cities, but "Jehovah" stays behind. Why is the third angel called Jehovah? because he is acting as God's mouthpiece. The "Word" if you will. In fact I believe that we suspect that this particular angel was "the Word" or Jesus prior to his being born as a human. No he wasn't Jehovah, nor was he Almighty God, but he WAS his chief spokesman. So he was addressed by Abraham in that way.
The Bible has things like this in it that SEEM to be contradictions, but really are not. Thomas no doubt KNEW that Jesus had always claimed to be the son of God, he also no doubt knew that he was God's chief spokesman. And he no doubt knew about the story of Abraham and "Jehovah" who came to warn about Sodom.
Is this confusing? Maybe a little. But not NEAR so confusing and unbelieveable as the Trinity teaching. Too many scriptures are directly contradicted for the Trinity teaching to be true.