I lived in Cambridge, MA until this August, and I concur with wck4. Almost everything is accessible by the T; driving in Cambridge and Boston is simply an exercise in masochism, and it is one reason I left Boston.
Harvard College is located right at the Harvard Square stop on the T Red Line. Can't miss it! The Business School is across the river, a short walk along JFK Street (from Harvard Square). Check out the Harvard web pages to see when tours are offered.
All of the suggestions about places to visit in Boston are great; The Public Garden, Boston Common, and Newbury Street are absolutely a must! If you are interested in American colonial history, follow the Freedom Trail (which will also lead you to Quincy Market and the North End).
I believe the Isabella Steward Gardner Museum is not too far from the Museum of Fine Arts which itself may be of interest (and is on the Museum stop of the E branch of the T Green Line). The Fogg is relatively small but worth a visit since you'll be at Harvard anyway.
In terms of places to stay, ideally you should stay near a T stop. Friends previously stayed at the Mariott (?) at MIT (right on the Kendall Square stop of the Red Line); there are a few hotels around Harvard Square, but those tend to be more expensive.
Enjoy Boston! I am visiting some friends there later in October...
Alex