I can only share my point of view, of course, but I'll tell you what stands out to me most about the two schools as far as their differences. (I go to Downstate, and visited NYMC a long time ago.)
1. Location. I am happy in an urban environment, so to me Valhalla felt absolutely suffocating. Couldn't stand it for one minute. Plus, where would you go when you needed a break from folks at school? NYC is far enough away that it would be a pain if you needed to get there often.
2. NYMC is a Catholic school. Frightening to me, delightful to others. At my tour my friend asked about how religious the school is and their answer was that the Catholic thing is only something they put on their letterhead, so I'm not sure if that's good or bad.
3. Price. Downstate is getting up to about $18,000 per year, but it's still cheaper than private school.
4. Cafeterias--they both suck!! But ours offers a little more
5. Curriculums--we're on the block system which I personally prefer.
Can't think of much else. I guess it boils down to where you like to live, what your personal philosophies are and what curriculum you prefer.