I live in a suburb of Boston and I have been contemplating the same question. However, I will more than likely apply to both BU and BC in the end. They are both excellent schools. While it is true that BU has long trailed BC in the rankings, BU is known for its quality of teaching. I think it is safe to say that they are both about equal, as far as rankings, although if you're interesting in intellectual property, BU has a "better" IP program.
For awhile, I was planning on only applying to BU, but now I am reconsidering. BU is located more centrally in the city. While this may sound appealing to others, it isn't to me. I'd rather live outside of Boston than right in the middle of it (hoping the cost of living might be a little lower and the traffic not as bad, etc.). Thus, I am starting to prefer BC. On the other hand, BC is a Roman Catholic school and I am Jewish. How much does this matter? Probably not at all - but it's something to consider. I am pretty sure I heard someone on this board mention that BC favors Catholics in the admissions process, but I highly doubt it.