Boston is an amazing city - it is walkable - and you will love it! I went to college in Boston and have settled about an hour north. When we go in to town we love the Boston Park Plaza - an older hotel with a lot of history and a great location - one block from the subway, great restaurants, close to the theater district, and a block away from Newbury Street for great shopping.
We also like the Boston Harbor Hotel - beautiful views and a short walking distance to Faneuil Hall and all of the touristy spots.
Then we love the Charles Hotel in Cambridge - great restaurants in the hotel, and close to Harvard Square (you have to go to Burdick's for their white hot chocolate - it is TDF!), and close to the subway into Boston.
You have to do the Duck Tours!
Red Sox tickets will be tough to get, but if you want to PM me, I can let you know where some spots are to get ummm, scalped tickets (I don't sell them, but I know where the sellers hang out). You can get tickets on ebay, but they will be wicked expensive, and if it rains, you are stuck with really expensive tickets.
We are actually going in this weekend for a movie and then pizza in the North End - you have to go to Regina's - the best pizza ever!