Irrespective of her last name, Margaret is most likely Thomas' first wife and arrived with him and their kids on these shores.
Why do we say that?
The Great Migration leaves it open, as do other genealogy works. Remember, genealogists have lead feet. We don't.
The studies, to which people point, all reference TAG 30:156 which does not make a definitive statement about the matter. The argument is that a church record of 1639 has Margaret showing up.
Consider, Thomas may have shown up at the Church in 1629, but he didn't deign to show up to be a freeman until 1637. Margaret may have decided to join much later, for the future of her family who did turn out to be successful in their own right.
Margaret was definitely ahead of her time and needs more attention to be given to her life.
Now, there is also a suggestion, in these studies, of a death of the first wife with Seeth's birth. This is not documented. It's pure speculation, folks, as far as we know (to wit, Great Migration, et al). TAG 30:156 does not tell us to not refer to Margaret.
The matter is open until there is further information that can be documented. In the meantime, we'll honor Margaret, with Thomas, as our ancestors.
11/27/2012 -- We visit the theme, one more. Anderson didn't leave it open. He actually made a hypothesis and stated a proof for his thoughts about a third wife. However, we don't agree with his analysis and will pursue the matter further.
09/16/2012 -- Of course, another reason that Margaret may not have been at church could be her maternal duties. I've not seen any depictions of kids in Puritan gatherings, except for older ones. Margaret, throughout the period of interest, had several young ones to care for. And, Thomas would have been there protecting them. Ideal couple, so to speak.