A local may give you better advice, but you can find the Alewife T-station pretty easily,
which has a huge parking garage and is right off the highway before you really get into
Boston.
From there take the Redline to Park Street. This is a decent stop if you want to
walk through Boston Common to get to Fanueil Hall. If you guys aren't so much
into walking, take the next subway to Government Center. This will get you as
close as you can get to Fanueil Hall by T.
If you can take the elevator to the top of the John Hancock building, that is a nice
view of Boston, not sure if they allow this after 911 anymore.
They also have Boston Duck tours, using a WW2 duck, goes in water and land around
Boston. This is over $30 a pop the last time I checked though.
www.mbta.com/traveling_t/schedules_subway_redline.asp