I just did a search and found that there is more than one Boston-Provincetown ferry. If you're taking the Boston Harbor Cruises ferry, here are their directions:
http://www.bostonharborcruises.com/Directions.aspx
A taxi will take about 15 minutes, and public transporation, again, about half an hour. For public transportation, catch the blue MassPort bus number 33 or 55 for the 5-minute ride to the Blue Line subway station. Then take the Blue Line "inbound" to the Aquarium stop (about a 10 minute ride once you're on the train), and BHC is right there.