AirBnB.
We live in East Cambridge right across from the Science Museum and know of a number of folks who AirBnB for very reasonable rates near us ($60-$100). And that would be prime for transportation and walking, too. And easy to get to with car - right off of 93. Additionally, you can check the site for Newton and Watertown availability - they're very near Waltham!
We'd offer, but sadly we're still prepping our place for AirBnB participation and don't have it complete yet! :(