First off, congratulations on your acceptances! I think your decision comes down to your timeline on becoming a PA and where you want to be post-grad. If you're set on working in the NJ/NY area, I would personally choose a school in that area so you can make connections with preceptors during your clinical rotations and potentially find a job straight out of school. To me, that crosses Rosalind Franklin off the list. There doesn't seem like a whole lot of advantages to RF over the other two other than cost, but you'll ultimately end up having to relocate there and then back to NJ after graduation, which adds cost on its own. And although Seton Hall is more expensive, having summers off means you can have some income if you choose to work during that time.
If you narrow it to Seton Hall vs. Cornell, the biggest difference is the timeline. If you attend Cornell, you'll be out an entire year sooner than Seton Hall when you factor the start date and program length. That translates an extra year working and income to pay back loans. Does your age play a factor here at all? If you're an older, non-traditional student like me, a shorter program that starts sooner is more desirable. From an outsider's perspective, Cornell seems like the better bet because of its lower cost, shorter timeline, and the fact that you will have housing covered with family members in the city. Yes, the subway will set you back about $120 for a monthly unlimited MetroCard, but you also won't be paying for car insurance, parking, or gas.
However, it seems that you have some genuine concerns about the program at Cornell and your overall feel of Seton Hall was more positive. I get the impression that your gut is telling you Seton Hall, and I think if you're okay with the longer time period there, it's worth the extra ~20k tuition in the long run. Ultimately, you need to be in an environment where you're comfortable and a place that you feel you'll be most happy during the stressful process of PA school.
I don't know if that helps or not, but hopefully it provides a little perspective from an outside standpoint. Best of luck in your decision!