I agree with daisygirl about the locations of the schools. NYMC is in a beautiful part of the country with really great facilities. The neighborhood at Downstate shouldn't scare you because it's a "really rough area", though. The only problem I have with Downstate's location is that it is hard to get to and is pretty congested. Other than that, it seems pretty safe to me. (But then again, I am a 6'4, 200 lbs male).
Also, the student-happiness issue is entirely subjective. I had just the opposite experience from daisygirl. The Downstate kids seemed enthusiastic and happy, while my NYMC tour guides were pretty blah.
It's a tough choice. If cost wasn't an issue, I'd probably take NYMC. For me, cost is an issue, so I'd take Downstate.