I can only comment in detail on Tufts. It's a great school though. Very expensive, as you know. But great area of Boston (which is an amazing city if you've never lived here). NEMC is a great hospital too, and I was very impressed by some of the other rotation options like Eastern Maine Med Center. I declined Tufts because I wanted a change of pace from undergrad. But Tufts was very good to me as an undergrad, and I know they're good to their med students too.
I know someone who goes to AE and really enjoys it. As a non-jew, I think she has a little trouble with the hours of the gym and libraries on holidays and shabbat. But if you're Jewish, you might not think twice about that. But it's a great school. My PI went there too and he loved it, and he's now a big doctor for Harvard.
Boston is a great city. The Bronx is fun too. I think you'd be making a good choice with either one. Think money too. Sorry I can't help with Stony Brook.