I have never lived in Boston, but I've rented in Philly and Chicago with my three big dogs (once in a one bedroom apt). Apartments.com is ok, but I always had much better luck looking in the local papers (you can do it online, and not for just the major area one, also for the weekly neighborhood ones). Apartments.com and that sort of thing only usually has huge apartment buildings with strict rules and higher prices, but you can find much better deals and bargain with individuals and small landlords who won't make you pay more for pets per month--just a deposit.
I always called any ad that looked good and didn't say "no pets"--if it's not specified, you can often talk them into it by saying how well-behaved and quiet your dog(s) is (are) and by offering references from past landlords. I've rented 4 places like that, and if I can do it with 2 or three big dogs, you can do it with one.