I don't know if the following opinions will help you in deciding, but I talked to four of my classmates. Two had been accepted to Downstate, Einstein, and NYU (one was waitlisted and the other was accepted.) They both came to Einstein over Downstate because they felt the location was better than being in Brooklyn. (They said Einstein had better and more affordable housing and since there is parking available, the incentive to have a car was nice.) One of my friends is from NYC and didn't want to go to school where Downstate is located and was also offered merit money from Einstein so came here over Downstate and NYU.
Of my two classmates that were waitlisted and decided to come to Einstein, one is Orthodox, so obviously wanted to be at Einstein for religious reasons. The other felt that the quality of education was better Einstein. The person felt that the location was better since he wouldn't need public transportation to get home when he wanted to go home and could also have a car to visit his signifcant other.
Personally, I really like the area I'm living. No, it's not Manhattan and yes, it's can take anywhere from 35-45 minutes to get into the city either by bus or subway. But, realistically, you're going to be a med student. It gets expensive to go to the city all the time and unelss you're skipping class, you really won't have all that much time to go play around in Manhattan until the weekends. I have a car in the Bronx and it's been really nice since I can see my significant other or go to the suburbs when I need to go. Grocery shopping and errand running have never been a problem for me. And there are times that I would love to be right in the city, but with as much studying and little time for myself as I have, I'd probably end up wasting a lot more time shopping, hanging out with friends, and procrastinating than I already do!
I've had an awesome time with the education I'm getting for it's ridiculous price tag, but I feel it's worth every penny. Besides having a weird schedule because our lectures are based on availability of doctors to lecture to us during the system based courses and conference sections, I can't complain about too much. Our anatomy course was probably my favorite thing about med school yet because I got to choose my lab partner and I had two other people in my group.
Good luck with your decision, it's a hard one to make, but I'm sure you'll be happy whereever you decide to go!