With car or without? Side trips to other places or in Boston proper?
Let's see: one day for the MFA and Gardner and the Commons; two days for walking the heritage trail; one day for shopping; one day for the Peabody and then bumming around that neck of the town; hmm. . .half day for Brookline and Coolidge Corner; a day for the Museum of Science and the Duck tour; half day for a game at Fenway Park; half day to meander Mount Auburn; half day to a day for the Harbor tour. . .
I'm sure I'm forgetting something!
If you want to do side trips, depending on season, Salem is a blast, as is anything on the Cape, or Gloucester. You can take the commuter rail or drive out to Concord and Lexington - lots to do there. Drive up to Portsmouth, NH. On your way back from the Cape (if you drove) Plimoth Plantation is fun. You can go out to Sturbridge and stay at (or at least tour) the Wayside Inn and see Walden Pond. (It's a hop, skip and a jump from Concord.) Right over the NH border is America's Stonehenge, which is great fun to tour.