I chose BC over BU for three primary reasons. The first is the reputation. I had lived in Boston for a decade and new that this market will always favor BC over BU. I chose a boston school because I wanted to work in Boston, so BC was the obvious choice. If I wanted to work in NYC, where BU places well, I would have gone to fordham which places even better and is easier to get into. That being said, I think it still takes relatively similar marks from either school to get a biglaw job; usually top 1/3rd.
The second reason I chose BC was the campus. There is a huge difference in the facilities available to the students. Visit both schools and see what I am talking about. While this is hardly a big thing to base a decision on, I like to study in a library, and I therefore need a comfortable and accomodating library and campus. BC offers that.
Finally, cost is a matter. I recieved the same amount of money from both schools, but living in Newton was a lot cheaper than living in Boston. I've managed to keep my debt low so that I can pay off my private loans as soon as possible. If I wanted to go into govt. work, BC also has one of the highest loan repayment programs in the country. While money should factor into such a decision, I don't think it should play a predominant role over other factors such as repuation and chances for success in whatever field you choose.
Both are great schools, but that is my take.