If you want to do string theory, go to Stony Brook, hands down. Austin has a good group, but the members do not publish as much as they did before, which is crucial if you want to get a postdoc; Cornell has two professors doing string cosmology and that is it (not to say that they cannot work on other topics within string theory, but that is what they do nowadays).
Stony Brook is way above those two. They have a very good group, they have the C.N. Yang Institute for Theoretical Physics and, starting from this year, they will have the new Simons Center for Geometry and Physics, for which they have hired one of the leading string theorists in the world to be its director (if you want more info about this new center, just google it). I don't know how mathematically oriented you are, so, you should take into account that Stony Brook, and to some extent Austin, focus more on formal work within string theory. Cornell less so. On the downside, I guess Austin should be a more exciting city to live in that Stony Brook (haven't been to either, I am an international student).
Good luck making the decision