Welcome to Boston! Yup, recent studies in WSJ show that Boston hotels on average are the same if not higher than that of New York City.
Your best bet is to either hope for last-minute weekend fares in a downtown property, or book in suburban areas like Westin Waltham, rent a car to drive in to places accessible to the T, and T it to downtown, Cambridge, etc. (Remember, T closes by 12:30 so if you plan to out late at night, keep a cab number handy or park in a garage.)