As someone who is familiar with the UMDNJ system, let me say that most people regard RWJ as being the #1 and NJMS as the #2. If you look at the admissions stats, that's just barely true, though.
Personally, I wouldn't want to live or spend a lot of time in Newark, which is a pretty dangerous city, so I'd choose RWJ. RWJUH is also a state trauma center (level 1) and the Bristol-Meyers Squibb Children's Hospital just opened up there recently. It also has a cancer research center and a ton of other things like that. RWJ is also a big research school, so if you're interested in research, then that might be another consideration. It's in a suburban area (oddly, the school is in a suburb while the hospital is in a city... go figure), if location matters to you. The hospital is less than 5 minutes from the school in the neighboring city of New Brunswick, which is a fun little city in itself. RWJ also shares its campus with Rutgers-New Brunswick, so you'll be in a nice little college environment if that's where you choose to go. And who doesn't love Scarlet Knights football these days, huh? 😀
NJMS is also a pretty good choice. I have a cousin who graduated from there. The location is what would bother me most, although my cousin said that the campus area is very safe and secure. The most glaring, obvious difference is the setting: do you want to be on a quiet Piscataway campus or inner-city Newark? They are both pretty stellar schools academically, so you wouldn't really lose out by choosing one over the other.