Lots of good advice here..but the one place the MBTA falls down, IMHO is the trip from the airport to downtown or Cambridge..need to take a bus to one subway, transfer, etc. With luggage. NOT recommended at rush hour. The one place to splurge on a taxi, if you can...
Boston is different even from other East coast cities. We have had guests remark that is seems more European- still lot of VERY narrow streets, cobblestones, etc. It is super walkable, however and full of beautiful things to see everywhere. Also, Bostonians move fast- you do not want to be staring indecisively at a menu board in a coffee shop, for example, if there is a line behind you!
And TOTALLY second the mention of Mike's Pastry, the BEST canolli !!!