Well, the whale watching is amazing, but it's best to check the season of when to go. Also, the food is amazing, not just the seafood, but also the Little Italy part of Boston -- oh my, it is authentic Italian food that melts in your mouth. Faneuil Hall is so much fun. The Irish area is amazing -- the wonderful blankets made on a farm from sheeps' wool.
Quick Tips:
Well, my first suggestion for Boston is bring comfy shoes -- your feet will thank you when you are done. There is a lot of walking, but you can walk from Boston Harbor to Fanueuil Hall, and then grab the subway to almost anywhere. My second suggestion is definitely try the first mom-and-popo restaurant you find -- I bet you won't regret it. Most of those places have the freshest food and old family recipes.
Don't be afraid to rent a car and head north of the city to Salem MA -- it is a very historic city, from old churches to the wax museums, it a blast! Especially on Halloween! They call Salem the witch city -- it has great historic information. And if you want, go north a little further to Gloucester MA -- can I say best seafood in the world! They basically catch it there in Gloucester Bay and then cook it.
Best Way To Get Around:
Walking if you're downtown and if it is to far, try a cab or even the subway. It's safe, somewhat clean, but very cost efficient. If going outside the city, definitely rent a car, but if staying in the city, they will charge a parking fee for the car!!