How about a tour that doesn't require either a bus or a boat? There is a great outfit called Boston By Foote that offers walking tours of several areas in Boston. We took the architectural tour and I loved it! I second a visit to the aquarium. It is worth the time and money. If you want something outside of the city, you can always go to Salem. There are numerous places to visit there that all have to do with the witch trials. The actual monument to those who perished is in Danvers, though, the place where the whole thing started.

Hotels in the city a very pricey so I wouldn't expect to get anything cheap. If you want to stay somewhere outside of the city, you can go a bit north to Salem or Danvers. Salem is a city but Danvers is more small town. You can park the car and take the T into the city and thereby avoid trying to figure out where to put that car once you've arrived. That is, unless you want and adventure and are willing to drive in the city!