its somewhat of a renters' market right now. though, it is the boston area, so its never going to be cheap... just less expensive. and of course, as the economy gets better (IF it gets better) rents are going to start creeping up again. i'm paying $610 for a big place right near brighton center and comm ave. i know of people paying just around $500 and living within walking distance of BC.
it also depends if you are going to have a car or not. if you are looking at BU and want to be close to the school, parking could be an issue and might end up costing you an extra $100 unless you are lucky enough to find an apt that comes with a parking spot. brookline is VERY hard to find a place with a parking spot. brighton is easier and allston even easier.
bottom line: i wouldnt let the cost of housing weigh too heavily into your decision. BU is a little more expensive since it is closer to the center of boston (assuming that you want to live very close to the school), but it is factored into their cost of attendance (the amount of money you are able to take out loans for). so in the end, maybe you pay an extra grand or two for BU vs BC. assuming you are taking out loans for 150k like most people, its a small fraction of your total cost.
however, housing aside, BC is infinitely better than BU. not that im biased or anything