It's a short drive into town from Logan International Airport, though the 'T' subway is the easiest way into the city. There's also a water shuttle from the airport to Boston's Rowes Wharf on the northeastern waterfront.
Boston is a compact city easily covered on foot. Driving is another matter since the city is infamous for setting the teeth of out-of-town drivers on edge. Cars might do for excursions, but for getting around the Boston-Cambridge area you're best off catching the T, the oldest subway in the country and one of the best. The T serves most areas of the city and Cambridge, and several lines head to outlying suburbs. The T is so useful that you can pretty much forget about using the local bus network, which can be confusing for newcomers. Taxis are plentiful but expensive.
Commuter trains go to some outlying areas (like Concord), but for most excursions you'll need a car. Boston has all the major rental agencies. Ferries go to several points around Boston Harbor. It's a three-hour ferry ride or a three-hour drive from Boston to Provincetown on Cape Cod.