Currently making this choice but waiting on $$$. Here's what I've been thinking!
Money comes first, all things being equal. Also, reputation is basically the same (maybe Cornell has an edge?).
But I vote Northwestern.
Location: For me, Chicago>NYC, maybe because I just know NYC so well at this point. Plus it's cheaper. I know Feinberg is in an expensive neighborhood but go a few miles west or North and things become much more reasonable, and a subway pass is included in tuition, so you'll already have it. Everyone I know who grew up or lives there now loves it, and I'm excited for something a little different.
Research: Heavy emphasis at both, with Cornell probably coming out on top, due to Tri-I and Cornell Tech going up! But, Northwestern is pushing HARD to expand their capacity, and they have the $$/space to do it. Currently a new biomed research center going up by 2018, recently renovated hospitals and lab space abound, and the RIC is getting a new mixed clinical/research hospital next year. Also, lots of crossover between the excellent Northwestern Engineering programs and the Medical School, which has some exciting research opportunities. Feinberg already puts out a lot of good work, and I think that's only going to improve.
Curriculum/Education/Hospitals: Cornell has 1.5 year, which I prefer, and you get an iPad. Northwestern has slightly less than two years, slightly more traditional, but cool things like the ECMH (longitudinal patient interaction with physician mentor). Both have PBL, strong research emphasis (Cornell might be slightly stronger), and concentrations if you want to focus your learning more. Hospital wise, Cornell has the huge Cornell Presbyterian, in the Upper East Side, while Northwestern has NW Memorial, Lurie Children's, and the Rehab Institute of Chicago, but all are in Streeterville. They do run programs at the County Hospital and the VA, as well as more rural sites, so there's the opportunity to see more diverse populations if you're so inclined. Both tend to serve rich people, especially Cornell with Sinai next door, but you'll probably see a lot of different stuff at both.
Also, at Feinberg, you can take one class per semester at Northwestern proper, so there's some great opportunities between the world renowned law, business, and engineering schools. But Cornell has Cornell Tech being built, so who knows what new opportunities that will bring!
Service: Didn't mention it, but I think it's worth mentioning. Cornell has the free clinic, and other teaching and service programs in upper Manhattan. That being said, the clinic is on the campus in the Upper East Side. Northwestern has 5 affiliated free clinics throughout the city, and many students work with the Chicago Public Schools as tutors/mentors. There's also recently been a lot of emphasis on health outcomes research, which is exciting to see, but it exists at both schools.
Student Life: Cornell has dorms, which are a blessing or a curse. Also, NYC is hard to beat for things to do, though it takes a little work to find ways to do them cheaply. There are also a lot of cool, non-academic groups at Cornell, like dodgeball or wine tasting. Northwestern has no housing, which is kinda obnoxious given that it's in Streeterville. But there are societies that group students, which I like the idea of, and they have events like the Olympics and In Vivo, which is a show. I know there are a lot of student organizations too. Students I met at both places were very nice! Also, you get a shuttle to Northwestern and can take part in their events, including speakers and things like Dillo Day (Anderson Paak and Schoolboy Q this year), which I really like.
So, pretty similar, but for me, the edge is Northwester. Beautiful new place (facilities + Chicago), better service opportunities, lots of new investment, and proximity to a university.
Either way, you're gonna rock it. Neither of these schools will hold you back! Good luck, and congrats!