I am in a similar situation for a PhD program (Chemistry)!
Trying to decide between Boston College and Johns Hopkins.
I'm originally from Rhode Island, so I'm really familiar with the Greater Boston area. I have lots of family and friends around the area, not to mention lots of Biotech/Pharma companies that I could see myself working at after graduation. But, the chemistry program at BC is definitely less "regarded" than JHU (not to say that the BC program is bad by any means). There's a few professors I could definitely see myself working with, but 2 of them are still assistant professors (i.e no tenure yet). The TA requirements also seem to be a little more extensive.
JHU is more of a "name-brand" and probably has the better dept. of the two. But, Baltimore is defintely a rougher place with less to do than Boston. The professors there have been there a little longer, so almost all of the ones I want to work for have tenure (or most certainly will get it in a year or so). I'd say the facilities are fairly comparable.
So, I guess what I'm trying to decide is if I am willing to give up what Boston has to offer as a city for a "name-brand".