I'm sure that lots of people are called Thomas without being a twin, and they're fine with that. No Thomas I know is a twin1). On the other hand, I am a twin, and neither I nor my brother are named Thomas. Is this meaning the primary reason for your naming concern? To answer your question, what do I think you should do:
Either change his name early, or stick with it. Let your gut feeling decide.
He has already heard you say his name a lot by now. The longer you wait, the more you'll confuse him if you do change his name. I think that his name will grow on you though, unless the name is already giving you goosebumps and making you uncomfortable - that's what I mean by "gut feeling".
Consider that if you change his name, you might have second thoughts about the new name, too. Make sure you're quite certain before you change it.
1) By the way: what would the other twin be named? They wouldn't have the same name.