I really think (wishful thinking but hey...) he's gonna come back to Boston.
First of all, I think at this point, they're in a better position to win than NY and Houston. I don't see Houston catching the Cards, where at least the Sox and Yanks are close to each other.
Next, in Boston, he won't have to be the ace. In NY, he's gonna be expected to carry the team and rotation with the trouble they've been having. I know Schilling would love to have him there, because Clemens mentored Schill when he was young. And Wells was an old teammate...though I don't know if they had a relationship.
I think the Boston ownership would be more likely to give him a situation fit to his needs with his family, than The Boss. They understand the big part of this for him is being able to stay with his family, and I think they would try every way to accomodate that. (Although I think that going away to pitch in another city for 3/4 months isn't that big of a deal, but he did miss a lot of time with them over the years.)
Clemens also has unfinished history in Boston. He could come back, get his Boston WS ring, become the Sox all time leader in wins, and have his number retired.
With all that said, Houston is the only team that can offer him to pitch with his son in the big leagues.