If you're just visiting for a few days, some of the things I'd recommend include:
- Duck Tours - they're a little expensive but SO MUCH FUN! it's the original city to have Duck boat tours, and by far the best.
-Museum of Science - especially if you're doing Boston with kids. Bonus, the duck tours leave from there.
-Museum of Fine Arts - one of the best museums I've ever been to!
-Wander around the North End and/or South End - two of my favorite neighborhoods. The north end has GREAT food, and the South End is great for strolling, people watching, going into cute little shops, etc.