Both are good schools that will prepare you well. They both have solid match lists into residency. That being said, I ended up going to RWJ, but it it more came down to 'feel' when I interviewed at both places. A large part of it was location and my interview experience. I liked Piscataway/New Brunswick much more than Newark. My interviewer also wasn't very nice when I was at NJMS, but that probably was my own personal experience.
There's also speculation that UMDNJ will be disbanded, and RWJ will merge with Rutgers. Whether that will happen or not remains to be seen, but it seems that it would hurt NJMS and help RWJ. Dr. Owen, the president of UMDNJ but who is more affiliated with NJMS, is adamantly against it, while RWJ is in favor of the move. While this has been proposed in the past and has failed, Gov. Christie seems to be strongly in favor of change, so it very well may happen.
If you have any specific questions about my experience at RWJ, feel free to PM me.