Hey, Alaskacub, welcome to the forum! Boston has so much to do that you won't be able to fit it all in unless you are there a long time. The Freedom Trail is the first thing most people think of but also consider taking a walking tour of the city (Boston by Foote) and definitely go the park and take a duck boat ride. It's a tradition. Visit Harvard Square (yes, you can walk around on campus and enjoy the history) and shop at Fanuel Hall.

Stick with public transportation, as Migflanker suggested, because parking is not only expensive but a nightmare to find. If you are bringing anyone young with you, the children's museum is one of the best I've ever seen and the aquarium is pretty cool.

Salem is a city that has several museums devoted to witchcraft history and the official monument is in the next town over, Danvers (Olde Salem Village is now called Danvers) but you will need a car for that. The train will take you to Salem station but everything is too far to walk unless you have an awful lot of stamina.