I'm not sure its that cut and dry. From anecdotal experience asking many people from the area, Tufts is a more respected healthcare provider regionally, although the name of BU probably carries more weight outside of the region. Tufts is also much more accessible via public transport (has its own subway stop), which can be a major convenience factor for students choosing to live further from campus. Location wise, BU is right on the edge between the nice but somewhat boring (and expensive) neighborhood of South End and Roxbury/Dorchester (project housing). The South End also has a reputation as Boston's gay neighborhood, not that there is anything wrong with that. I lived right near the edge of South End and roxbury and while I never felt threatened, crime is definitely an issue in that area, people get mugged for cell phones and ipads frequently.
I'm not sure that the research rankings matter at all, there is plenty of research going on in Boston and there is nothing preventing Tufts or BU students from researching in labs in either institution, or @ MGH, BWH, Childrens, Harvard, MIT etc etc. If you had a very strong interest in emergency medicine BMC is a safety net hospital and may take the edge there.
I'm not sure there is a clear cut "no contest" victory for BU here. I think it probably comes down to individual fit... At the very least I would say don't decide on BU solely because you think it may offer better research opportunity because I can tell you first hand that in Boston students often end up researching in labs not affiliated with their home institution. If I had to make the decision I would look more closely at the curriculum, financial aid, extra-curricular opportunities etc. and also which may offer more opportunity for whichever specialty I was considering to pursue after graduating.
edit: also wanted to add RE: research rankings, not sure how thats determined but I'm pretty sure the major factor there is funding, BU's big jump in recent years is probably due to the opening of the NEIDL facility, (
http://www.bu.edu/neidl/) I'm not really sure how much this has actually changed the research landscape for BUSM students