I've met some people from BC and I've obviously had a lot of contact with people at BU. I can't say that I've noticed any group-wide differences though.
I would say that firms seem to look at the schools differently. Boston seems to like BC better. New York seems to prefer BU. The schools are pretty close in prestige, but look at some of the firms you might be interested in and take note of where the people are from - and remember that people do like to hire from their own school.
The biggest difference is probably location and facilities. I've never been to BC, so I don't know what it's like - but there's a reason I've never been there... it really should be called "NC" (Newton College). Okay I'm going to get in trouble for saying stuff like that.
I'm sure you're already aware that, physically, BU is a giant ugly tower. This provides for great views and notoriously bad elevators. It's a lot closer to the rest of Boston though.
As for BU's health care program - I don't know much about it. In general, "programs" in law school don't mean that much. They're often just a couple famous professors or something like that. BU does have a medical law journal that is well regarded: http://www.bu.edu/law/ajlm/