We would highly recommend Minga and Jonathan's home. It is a very charming period home which has everything you would need to have a comfortable and homely place to stay.
The location in Cambridge is perfect for exploring The various parts of Boston. The subway is a 5 min walk which also then gets you to the airport. MIT is walkable. Harvard a couple of stops. There's a couple of nice breakfast /brunch places nearby - cafe Luna and friendly Toast. Lamplighter brewery is also excellent and only 15 min walk.
We had a late flight out of Boston and Jonathan kindly allowed us to stay a bit later which allowed us to explore a bit more of the city before our flight.
5 star stay and great value in Boston!