Since I did the entire interview circuit in Boston, I thought I'd chime in 🙂.
I agree that Brigham is the stongest, followed by MGH. They are both excellent (excellence in clinical skills, research opportunity, and didactic sessions), but different atmospheres. BWH is known to be more resident-friendly, though personally I have found them both to be. BWH is a program from which you can do anything (they have 2 great primary care programs and a fantastic fellowship placement history). MGH is one of the few programs left (along with Hopkins, etc) that still have interns taking overnight call and doing admissions "alone" (a resident is always nearby) pretty much from day one. Great for those who like to work independently. Good primary care track and excellent fellowship placements.
These are followed by BU and NEMC, both of which you will work hard and learn alot. NEMC is unique in that you the hospital is arranged by specialty (so when you are on wards you will be on GI vs Renal vs onc, etc) and you are learning from specialists in the fields. BU is unique in that it is our last city hospital and the residents really regard it as such; thus, you see a large portion of the indigent population here. BIDMC is also very good. Great for primary care and they seem to be recovering from financial problems relatively well.
Some other programs that are just outside the city:
Lahey Clinic is by far the strongest program in this category. If it were in the city I think that it would be on the same tier as BU, BIDMC, and NEMC. It is unique in that it is a smaller program that all the Boston programs (about 30 residents). Good primary care training and good track record for fellowship placement (cards, GI, etc). All the workings of a major "city" hospital (in terms of 24 hour ancillary support, radiology, tertiary referrals etc) in a suburb.
Cambridge is a good program, just very small in terms of resident number and hospital size and functioning. Good primary care training. Mount Auburn is also a nice program, a bit larger than Cambridge. Also good for primary care.
Hope that this helps! 🙂