We visited Boston in November - great place.
Stayed here : http://www.lenoxhotel.com/ but check otel.com and Expedia.co.uk to find the best price (I asked the hotel for a price match and they couldn't get close). Don't forget about cash back potential from Expedia if you go via TopCashBack.co.uk. The Lenox is spot on for location - great for eating, shopping (it's right next to Lord & Taylor which my misses loved, not to mention Crate & Barrel), and the subway (the T) for getting around.
Get a Charlie Card for the T - allows unlimited use on the subway and buses which can be nice to give the legs a rest. You can also get out to Harvard on it - that's a good morning.
I enjoyed the Boston Aquarium, personally better than the Natural History Museum at Harvard.
Try Mike's City Diner (http://www.mikescitydiner.com/) for breakfast - I tried the three blueberry pancakes and thought I was going to explode. If you fancy a cheap tea one night, go to the Quincy Market Hall - take your pick from all the different food places (ace clam chowder).
http://www.atlanticfishco.com/ is crawling distance from the Lenox. Also worth going up the Prudential Tower at night for a drink. Minimum spend per person if you want a table but you can have a few drinks at the bar.
Don't forget to visit the Sam Adams for the brewery tour (use the T). Free for the short tour and then free beer tasting (don't forget your ID though)
I've got a Word document at home listing all the places we found to visit, eat etc