There are lots of places in Boston to go and see it depends on what you are into. I would recommend the freedom trail; it will fill most of your historic needs. You can see the Constitution, Bunker hill Monument, Quincy market/Faneuil Hall, Old City Hall, Boston tea Part Site, etc., etc., etc. Boston also has some of the finest museums in the country, the MFA, the Science Museum, the New England Aquarium.
If you want to venture a little out of Boston you could head to Lexington and Concord, and see the battle road and the site of the start of the American Revolution.
I would recommend trying to get a few sox ticks if they are in town. Just to see Fenway park is a trip in itself. If not, do the tours that they have, you can get more info on the web site www.redsox.com
In the Bar's department, if you are looking for traditional Boston bars, you should try the Faneuil Hall area. The bell in hand is a traditional Boston bar in the old part of the city. Also in this area are Purple shamrock, the tap, Hennessey’s, etc. for dance Style bars (not nightclubs, bars w/ dance floors). For more traditional pub style places with background music, try the Newbury Street, commonwealth Ave. area. They have more pub style places that sell food during the day and drink at night.
As for night clubs the two best areas are Lansdowne Street near Fenway Park, all clubs, and the theater district.
Boston is loaded with places to get a drink; you can go from "hole in the wall" dive bar to super up-scale need a name to get in places.
I would recommend not going to the original Cheer's, it is not what you think and nothing like the show's bar. There is a cheers in Faneuil hall that will give you a more TV like feel, if you have to get your cheer's fix and t-shirt go there instead.
If your look for a great place to eat then the North End is the place to go. Tons of small, family owned, traditional Italian restaurants. If you want an authentic New England meal go to Durgin Park, and if you want New England fried fish and clam chowder head to the North shore and try a few small places there.
Last but not least, never drive in Boston. You can literally walk from Harvard University to Fenway Park in about 15-20min. You can also take the subway, locally known as the "T." The public transport is safe and efficient in Boston. Most stops are within walking distance of each other. If you want a little more information about things to do I would recommend checking out the Boston section on tripadvisor.com. The forums have tons of good ideas.