Nothing in Boston is really "inexpensive". The Harborside Hotel is on the low end for the city and is very close to the ferry. Many folks complain it's very noisy plus there are some other problems, so I would check the reviews first on this sight first and see how they "fit" you.
Try http://www.boston-bnbagency.com for some nice places. You will have to Google map them or ask the agency about their location but a taxi from any location to the ferry might be worth it!
Acc'd to posts here, the Westin Waterfront is running some specials. You might try them. Also, Priceline or Hotwire may get you a discount on a city hotel.
Which hotel is most convenient depends upon where you're leaving for Provincetown from; Commonwealth Pier (Bay State Cruise Co.) or Long Wharf (Boston Harbor Cruises). The Westin Waterfront is convenient to Commonwealth Pier and Harborside Inn is convenient to Long Wharf. Since nothing in Boston is that far away, another possibility for a cheap room is John Jeffries House. They are very inexpensive and located next to the Charles St. subway stop. Unless you have a huge amount of luggage, it wouldn't be difficult to get to either pier by subway in about 15 minutes, although either trip requires train changes.
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