Hellojed,
I thought I'd give the MCW side of things since I am now a 4th year there. I interviewed at both of these schools and know a little about NYMC as well. Just so you know, I am not from Wisconsin or the Midwest and actually went to high school on the east coast and college in California.
Students: Generally a happy bunch, good administrative support of student body. Probably about 10-20 really competitive people per class who kiss ass and annoy everyone else. The majority are laid back and work well together. In a large class of 200+, there are often cliques formed. I personally had a group of 10-15 people that I hung out with most of the time and 4-5 really good friends.
Pre-clinical: The first two years (pre-clinical) years were a great experience for me. The curriculum is somewhat traditional, but more and more PBLs and clinical courses are being added. The monthly block exam system worked well for me because I could slack off for 2 weeks (and miss a lot of classes) and still be able to do above the mean on exams. There is a great note-taking service that everyone participates in which makes up for any missed lectures. The new lecture hall is state of the art.
Clinical years: I don't think NYC has that much of an advantage in terms of the types of diseases and patients seen (Milwaukee is a decent sized metropolitan area of >1.5 million). The main hospital, Froedert, is very new and has some of the best facilities of any of the schools I've been to (I've interviewed at 16 different places for residency and 5 for med school).
City: I was apprehensive about Milwaukee as a town when I first moved here. It really has grown on me and has a variety of things to do. It is possible to have an active social life. I'll admit, its no NYC. If you crave big city life, Chicago is 1.5 hours away.
Housing: The housing at NYMC seems cool, but I can't imagine living with all medical students in the middle of nowhere. I need some outside contact. There are plenty of great apartments near the campus or in downtown (20 minutes away). No horrific traffic like in NY. Did I mention the prices are great?
I think both schools will offer you a great education. I personally have been very happy with MCW for the past 3.5 years.