RWJ has a better rep. in general, but this is mostly in regards to research. The student population at that school has a higher GPA/MCAT (I believe). NJMS, on the other hands, is popular for its clinical experience. Both ways, however, I don't think you can go wrong.
Yet, looking into the future, there could be some changes. For one, there has been quite a push to combine Rutgers-Newark, NJIT, and NJMS into one school. This would substantially boost NJMS in some aspects, but have drawbacks in others. Yet, I'm not so sure whether this would happen during the years that you would be there, but Rutgers seems to be pushing for it.