Most of the attractions on this itinerary are within walking distance of each other. For the Harbor Cruise, consider taking the subway or a taxi to the wharf. The subway is very reliable and affordable at $2.75 per ride, and taxis typically cost $10-$20 for a short ride within the city. If you'd like to explore more of Boston's neighborhoods, consider renting a bike or using a ride-sharing app like Uber or Lyft.
If you have more time, consider adding a day trip to nearby Cambridge to see the famous Harvard University campus and enjoy the trendy restaurants and stores on Harvard Square. If you have less time, you may want to skip the Museum of Fine Arts or the Harbor Cruise.