You need to base what you will be doing on your interests. If shopping is your thing, then Fileen's basement is a must do. If it's Science type things, then the museaum of science or the computer museaum is the thing to do. If it's history, then there is certainly lots of that there, if it's sports and the Red Sox are playing, then that's the place to go. Likt Italian food, then head to the north end for dinner, seafood then there are lots of great seafood places too. Art and the rest - Plenty of choices there.
There is too much to do for any interest, so pick and choose based on what you really like.
There was a three perfect days story on Boston -
http://www.hemispheresmagazine.com/three/boston.htm that may help you figure it out.