I've stayed at three hotels in Boston - the Four Seasons, the Club Quarters, and the Copley Plaza. The Four Seasons was the best one because they treat you like royalty. I asked for an upgrade upon check-in, and they gave me a huge junior suite. The room was amazing as was the bathroom. It had a huge spa tub, scale, and lots of different bath oils and soaps. Plus, it was convenient to the park and to downtown. The hotel actually provided free transportation to my office in the morning which was a nice bonus. On rainy mornings, a bellhop hands you a gorgeous full size umbrella. The city itself was beautiful and was very walkable. The Cheers Bar was fun.
The NE Clam Chowder at Legal Seafood and Turner Fisheries was amazing, but I equally enjoyed the American fare at Joe's American Grill. Plus, Joe's had the best desserts. Boston also has my favorite bagel store - Finagle a Bagel. I love their energy bars!
Fanueil Hall is my favorite attraction. The shops and foodcourt are wonderful, and you get a good view of the Harbor there.
Quick Tips:
American Joe's Grill
Turner Fisheries
South of the Border Restaurant in Cambridge
Walking around the MIT and Harvard campuses
Catching a Red Sox game at Fenway
Filene's - the city's oldest department store
We watched New Year's fireworks at the Harbor along with thousands of other screaming, freezing people and had a great time.
I got the hang of the subways pretty quickly, but the system is a little tricky since you need to know if you are going inbound or outbound.
Best Way To Get Around:
Walking is great as long as you can stand the extreme cold. Otherwise the T is an extensive system. There are horse and buggy rides. Boston is notorious for having horrible drivers, and it has many unexpected one-way streets, so it is frustrating to try driving around if you aren't familiar with your route. I recommend leaving the driving to others by taking public transportation or walking. Also, from the airport the shuttle busses only charge about and they get you to your hotel very quickly and are a much better value than the + cab fares.