The MBTA subway system will probably play a major role in travel in the game. Since the game starts in outer Boston, you would take the Green Line Trolley (or at least walk along the rails) to enter the city. That or you could walk along the Mass Pike I guess.
Stuff in
bold are confirmed locations or mentioned in official concept art.
The Green Line will take you to places like
Fenway Park and the Boston common. The
Mass. State House is north of the Common and the
Old North Church with
The Paul Revere Statue is north of Haymarket Station.
Switching from the Green Line to the Blue Line at Government Center Station will take you to State Station, From here you can find places such as The Old State House and Faneuil Hall. Keep going and you will get to Aquarium Station where you can find the Waterfront with locations such as the Aquarium and the Wharf. If you continue on the Blue Line you will cross under the water and get into Jeffries Point with
Logan Airport nearby. Although it would be easier to get to Logon with the Silver Line.
If you get on the Orange Line, you will go north into Charlestown where you can find the
Bunker Hill Monument to the east, if you walk South from there you will find The Charlestown Navy Yard where the
USS Constitution is supposed to be (although since it can fly now for some reason, the ship might be somewhere else.)
The Red Line going North will take you to the Hospital and further on the
Massachusetts Institute of Technology, while going south will take you to the J.F.K. Library and Quincy.
This is just a basic overview of some of the locations that can be accessed with the subway system.
Yep I can just imagine 'em. They better carry baseball bats. To quell their centuries-long anger, a hunt for a signed baseball by...hmm, Babe Ruth maybe? Not enough? 
