If it doesn't matter to you where exactly you stay, I would recommend using Priceline or Hotwire to get the best deal for lodging. There are several websites that can help you with either of those, I like using betterbidding.com whenever I'm using PL or HW.

For tips on things to do while you're in Boston, there are some threads in the New England Master Thread that might help you get some ideas. Just be advised that Labor Day weekend is a very busy time in the city.