From my trip to Boston at the weekend I would recommend The Gryphon House Bed And Breakfast, in Back Bay. Friendly staff, lovely rooms, nice breakfasts. It’s not in downtown but the subway station is just round the corner and from my perspective the MIT campus was in easy walking distance. And if you are interested in baseball, the RedSox stadium is practically next door.
Another recommendation would be Joanne Wong of
citi-habitats.com, a New York real estate broker, who managed to find me a half dozen places to see at a few days notice that met my requirements and included landlords who did not mind the lack of a US credit history, walked me through the letting process and kept it all simple for me. Following up with a card and a voucher for a department store was just icing on the cake.