Both programs are mediocre even if they're the 2 top academic programs in NJ. Here's a summary of both places.
RWJ
1. Better reputation in NJ and throughout the northeast.
2. It's a hybrid model where most attendings are also in pp so if you come here and make connections you'd find a great pp gig in NJ.
3. 4-6 residents per year with 150 (mostly pp) faculty. However, they filled 0/4 spots in 2015 and had to scramble. Most residents seemed happy during interview day and the majority go into private practice after fellowship.
4. One thing that was extremely off-putting was that one of the interviewers came across as malignant (brown dude, I forgot his name). I've heard bad experiences about him from other applicants as well. However, the other interviewers seemed chill. I heard he was the old PD so it's great that he's not in that position anymore.
5. Has an IR fellowship program.
NJMS
1. Located in Newark although close to NYC.
2. It's a small academic program without much research going on.
3. 4-5 residents per year with 25 faculty. Based on their website, most residents are FMGs. On interview day we only saw the chief resident who gave us a tour. It felt like the other residents were hidden away which was a red flag.
4. The PD and chairman seem cool. One attending who interviewed me (old white guy) seemed malignant though.
5. No fellowship program
Both places have level 1 trauma centers, so you'll see a little bit of everything. On the trail I've met med students from both programs, and based on what they've told me, it sounds like the residents are required to work really hard at NJMS with a rough call system, whereas RWJ is more of a "do as much or as little as you want" program. If you have better choices, feel free to list them, but if these are your top 2 then I'd go with RWJ.