Peg, have you considered moving south? Sharon, Canton, Franklin, etc, only 1/2 hour out of Boston and the T runs to all these places. The T runs as far south as Attleboro, MA, but that town's kind of a pit...and it would be an hour commute anyway.
The rents are not a heck of a lot better; when I looked a few years ago it was easily $1,000 a month for a two bedroom apartment, but there might be something. Manville is very affordable but I'm not sure if they have a T station.
Good luck, especially with your kitties. We have four ourselves or I would consider offering a temporary home to some of yours. Apartment hunting with pets is virtually impossible.