Traveling to Boston...any suggestions?

Hi, I'm planning on visiting Boston this summer with my family. We are currently looking for hotels. We would like to know which is the best area to book a hotel. Any suggestions? We are interested in some place that is VERY centric and not too expensive... We are mainly interested in seeing historic sights and museums what sort of things would you guys recommend. I would also like to know which are the best methods of public transportation i.e. metro, buses, walking? Thanks!