Charles River makes all the difference. Strips of grassy parks that follow Charles is just awesome. go there during the fall season and you'll see some wonderful views with students playing various activities, reading books, and a nice walk along the river.
Historical baseball stadium, Fenway Park. Even if you don't like baseball, go to a game just so you can tell a baseball fan that you've been there. One of the very few great fan centered baseball stadiums. Fun local atmosphere during games.
Museum of Fine Arts (MFA). They have a very respectable number of worthy artworks and ancient artifacts on display.
Freedom Trail is available for those who are interested in history (what history?!?) of Boston . . .
Harvard Square is a must for its atmosphere and its spirit.
Quick Tips:
No need to spend more than two full days here. As much as I love this town, it is better to live here and absorb and experience the atmosphere of this great young town. But for those who are looking for tourist attractions, there ain't much here. Just max out your two days here and go on somewhere else like NYC.
Best Way To Get Around:
Walking and Public transportation(The "T") is the best way. Parking is horrendous even for locals in Boston. The T will take you virtually anywhere and you can walk from there. Bus is more seldomly used, but they are very accessible. Boston is a small city and it will be easy to get anywhere from anywhere.