Planning a Trip to Boston, HELP?!?

My fiance and I are trying to head to Boston this fall. What is the weather typically like the last week of September, 1st week of October? Also, we are planning a day trip to Boston so beside the Sam Adams brewery (:D) what other places should we check out? We are also taking a day trip to Salem, and a 2 day trip to Plymouth. We both really like history and outdoor activities. THANKS!