to answer the original question; I would say that BUMC is the better program overall, with 3 different hospitals (BUMC, Boston City, W. Roxbury VA-shared with BWH and BIDMC), the oldest primary care track in the country, and the opportunity to serve a really diverse population. However, if you like the idea of doing subspecialty ward rotations beyond Cards; Tufts-NEMC might be a better choice, and NEMC is particularly strong in Nephrology, GI, and ID.
I agree with considering Lahey and Mt. Auburn as well; don't know much about the latter, but Lahey is a program with a strong reputation in New England, and an OK national rep. Their GI and Cards dept. are particularly strong (the former nationally ranked with very high-caliber fellows), and several Harvard med grads have matched at Lahey in the past few years. Although NEMC has the better national reputation; Lahey is well-regarded in the region, has excellent fellowship placements, and people seem to be very pleasant there. I would actually pick Lahey over NEMC myself b/c I had some awful experiences in other depts. at NEMC and have heard that the residents are not that happy at NEMC, but everyone has a different preference.