I'm not sure I'd include Boston in this. It has two zoos and the one in Franklin Park is better than it used to be, but neither one is very good. I would, however, add Chicago. It has two fine zoos in Lincoln Park and Brookfield. The former is right in town and is free...parking is quite expensive but Chicago has a decent transit system and it's easily reachable by bus or a brisk walk from the L train.
Brookfield is in the suburbs but the commuter train stops nearby.
Brookfield is in the suburbs but the commuter train stops nearby.