This is actually a tough one, I think. First of all, it's important to make sure biographies or notes or something is included with each creator. That way the two can be distinguished. Then you have to make it possible to pick them out of a list. In order to keep the name as close to the one with which the artist is most commonly credited, I would say mark one as Mike Thomas (01) and the other as Mike Thomas (02), with the 01 being whichever was born the earlier.
However, I've been doing a little digging into the inking jobs credited to Mike Thomas on the Mutanimals, and they were wrong on our site. It wasn't Mike, but Brian, Thomas who did that work. Same goes for the Teenage Mutant Ninja Turtles stuff. So, when those are corrected, Mike Thomas will have only colorist and cover credits.
I don't actually think there are two Mike Thomases.