NJMS - no question. Their match list punches well above their weight, cost of attendance is significantly cheaper than NYMC, and you'll get some of the best clinical experience in the region. NJMS is easily one of the most underrated medical schools in the country, and I think residency directors recognize this.
The exposure you would gain from working at University Hospital, the ability to do your clerkships at HackensackUMC (one of the best hospitals in the metropolitan area), and the research opportunities available through Rutgers make NJMS an obvious choice. The Newark demographic is also diverse, medically underserved, and immensely underprivileged, making community service projects easy to implement.
If you take a glimpse at NJMS's match list, it almost leaves you slack-jawed by how impressive it is (especially if you're interested in matching somewhere in NYC). Also, if you have an interest in specializing in neurosurgery, NJMS generally ties Hopkins in the number of neurosurgical placements each year. The only foreseeable negatives of attending NJMS are the city of Newark, outdated facilities and a chaotic clinical environment. Other than that, I don't see how NYMC, Westchester Medical Center or any of its community affiliates trump NJMS.