That's wonderful!! I went to Northeastern University in the Back Bay of Boston and my father worked at M.I.T.
Both Harvard and M.I.T. are in Cambridge which is across the river from Boston. The campuses are about a mile? apart but walkable. You can also get there by subway but, if I remember correctly, its only one stop and not worth it. Treat yourself to a taxi or find a bus route that travels along Mass Avenue.
The MBTA subway system runs from the airport (although the first part might be by bus) into all parts of both Boston and Cambridge; you can probably find a subway map on a Boston homepage. As for hotels, do a search on Logan airport and I think you'll find that most of the popular hotels are nearby, probably with shuttles from the terminal to the hotel.
As for renting a car? Don't! Not for this short a stay. Driving in Boston is an adventure not for the faint of heart!!
Shame you only have two days! There's a lot to see, all of it accessible by subway. The Boston Museum of Science; the Museum of Fine Arts; or, just take the subway to Boston Common and look around!
Hope you have a wonderful time! And, that your son gets into M.I.T.!!