I interviewed at both, know both well, and knew people at both schools, but wound up going to another school. Go to UMDNJ-Newark, it is a better value, if you are a NJ state resident. It's like choosing between a toyota camary and ford taurus, and the taurus's sticker price is 2-3x as much. Which car/education would you buy? No reason to carry around so much debt on your back. If you are talking about Columbia, Cornell, Einstein, Mt. Sinai or NYU vs UMDNJ-NJMS, then it is a different story and the decision process gets tougher.
UMDNJ-NJMS is cheaper and has strong affiliated hospitals. I actually think it has a better reputation than NYMC in terms of residencies/specialties as well. It will be tough @UMDNJ because of some of the scut you will have to put up with. You will get a good education at a much better price. At Newark you will see all kinds of crazy pathology. You won't regret this one bit. NYMC is a decent school, but not worth the dough, unless it's your only admission or you want to live in the village (St. Vincents) during 3 and 4th year and pay lots of $ to do it.
One more thought. Ask for a copy of the match list of the class of 2001 at both schools and make sure they include both the specialty and the associated hospital at which those people match. Look at the quality of hospitals matched. Less important but still worth a look, see how many people matched into difficult to match into specialties (v.high unmatched rate) such as Dermatology, Orthopaedics, ENT (it's official names is Otolaryngology), Plastic Surgery, Radiation Oncology, Radiology and Opthamology. Also make sure you take into account class size for the above calculation.