We got married at the Commandant's House in the Charlestown Navy Yard which is very close to the Boston Harbor. We were even given the opportunity to take photographs on the USS Constitution which was really cool.
For our rehearsal dinner we had a dinner cruise with the Charles Riverboat Company that left from the Navy Yard and went around the harbor and Charles River.
How about St. Charles river front? I got married at the Sonesta Boston and love looking back into my wedding album at the spectacular Boston skyline and the St. Charles River. All the guest loved the food and attention to detail they offered. Save your self the hassle and check into wedding packages. Trust me you wont regret someone else doing all the work. Also they have great deals for any out of town guest that will be attending. http://www.sonesta.com/Boston/