I stayed multiple times in Omni Parker Boston, a lovely, historic building in downtown. I think it runs a bit expensive, though. We always go for a conference and get a special conference rate.
http://www.omnihotels.com/Find.....House.aspx
I also stayed once at Boston Marriot Long Wharf. Very nice hotel but not historic, right across from the Aquarium.
http://www.marriott.com/hotels.....ong-wharf/
Finally, in my most recent stay, I stayed at this newly renovated Holiday Inn in Brookline. It is in a relatively residential area but there is a T stop right in front of it and it is extremely reasonably priced:
http://www.ichotelsgroup.com/h.....otel/bklma
I found these last two hotels through Priceline. I would strongly recommend Priceline, "name your price" option. Basically you choose an area of the town that you want to stay in and the lowest star level that you are willing to accept. Then you make an offer and if any of the hotels with those specifications accept your offer, you get a reservation. The only downside is there is no cancellation and you can't choose which hotel you will be staying in in advance. But I have previously used priceline to reserve room in various parts of the country, sometimes with almost up to 60% discount on regular prices and I always stayed in comfortable, clean , nice hotels.
This is the priceline website:
http://www.priceline.com/
And this is a great forum:
http://www.betterbidding.com/
If you want to use priceline, I'd suggest you poke around this website and familiarize yourself with the process beforehand.