Boston is so filled with history that It's hard to limit yourself!
We like to start at the Bunker Hill monument and see the USS Constitution. Then work our way south, as traffic can get thick as the day goes on. But that part of the tour while certainly hisorical, is really not much more than a 'look' there it is!
The Fanuel Hall Quincy Market area is a nice combination of architecture and shopping.
However, I do love the 'Duck' tour, and if you have time you can go to the observatory of the Prudential Center and have a magnificent view of the city. This is one of the boarding sites for the duck tour.
You can also do the trolley tour and get off and on the trolley all day for one rate. Here's the link
for that. Just make sure you have fun, and be glad that you don't have to try to park here! The cost of an all day trolley is about the cost of a few hours for your car to sit!