Off the top of my head:
Isabella Stewart Gardener museum. A random collection of objects that Mrs. Gardener found on her travels in Europe--paintings by the masters, tapestries, ceramics, floors, walls, fireplaces, wrought iron gates, snuff boxes, you name it--all gathered into a house she designed along the lines of an Italian villa. The gardens are lovely, and the story of her life is fascinating.
Very close to it is the Museum of Fine Arts.
Fenway Park, which offers a behind-the-scenes tour on non-game days, is also in that area, as is the Fenway Rose Garden.
Moving closer to downtown, in the Boyleston Street area, there's the Boston Public Library. They give free tours of the art and architecture of the old building, which had paintings and sculptures by several famous artists. The old part of the library fronts onto Copley Square, where street artists and open markets are held in the summer.
There's lots of interesting shopping and window shopping on Newbury Street, one block over. And a lot of other shopping in the general area.
Downtown, there's the Public Garden and the Swan Boats, the Boston Common, the downtown shopping area, Beacon Hill with lots of old houses, the State House where you can take a tour, the Duck Tours which give you a tour of the city and then plunge into either the Charles River or the harbor in amphibious vehicles, and more shopping.
Over by City Hall, there's Quincy Market with lots of restaurants and more shopping.
Plus the Aquarium (great penguin exhibit), the Children's Museum (if you will have kids along), the Science Museum.
If you have time, you can go over the river to Cambridge--Harvard, more shops, MIT museum, tons more historical sites.
I'd advise getting a day pass for the T, and using public transportation to get around. On-street parking is scarce and parking garages charge over $30 a day. And with the plethora of one-way streets that never go in the direction you want, driving is a hassle.