When in Boston there’s tons of hotels and even airbnb’s that you could stay at. Airbnb you could stay anywhere in the city virtually I would recommend near parts like the north end or by the business district. Today I will recommend various hotels in various price ranges that are in nice areas with plenty to do around and near.
For a higher budget ($223 a night) I would recommend staying at Revere Hotel Boston Common. This fine hotel with a lovely restaurant, great pool, hangout area at the top of the building is tucked right in busy downtown Boston with Faneuil Hall near by. 
For a more mid range price ($162 a night) a would recommend staying at The Westin Boston Waterfront. This great hotel is right near the Boston Aquarium right near Faneuil hall and the north end with plenty to do nearby. This hotel is bayfront and boasts a lovely pool and indoor and outdoor dining areas. 
Finally, for a lower budget ($69 a night) I recommend staying at The Farrington Inn. With this great location, 2 miles from Harvard Square, 4 miles from The Museum of Fine Arts and it is 6 miles from the New England Aquarium. This is your basic hotel you get what you pay for, a nights stay and a great location and good service. 