So I wasn't going to post, as I'm unfamiliar with both hep/astro theory, but since no one else has said anything yet, I'll give my two cents (which you should take with a large grain of salt) because I was in a similar situation (check my post on the acceptances thread: http://www.physicsgre.com/viewtopic.php?f=3&t=99428&start=100#p199971
I'd probably go with Stony Brook since I have no idea about the people you are interested in working with. My main reason for this is because:
1. Stony Brook and Northwestern seem similar enough in rankings to not really matter (bar nuclear?).
2. Stony Brook seems to offer you 2 years (but allows you to finish earlier if you want), whereas Northwestern seems to only offer 1 year (including a summer).
3. Stony Brook seems to have more alumni from their MA program and they have gone to a variety of places, although most trickle into Stony Brook PhD, which is still amazing. (https://www.physics.northwestern.edu/people/masters-alumni.html
4. Although Northwestern is 30 minutes closer to a big city (Chicago) and UChicago which is great for Astronomy/Cosmology I hear (they have the KICP), I'm not so sure how much of a factor this is to you.
I take it you ruled out CSULA? I heard they have an interesting connection with NASA.