The Marriott Long Wharf is a very nice hotel. I haven't stayed there in a few years, but I'm sure that it is still a very nice property. It is also conveniently located near many tourist attractions. Legal's Seafood is close by, as are all the great Italian restaurants in the North End.
I recently stayed at the Omni Parker House, which is an older hotel. I thought that the service was great, and the staff incredibly friendly and helpful. My room was a bit small, but nicely decorated.
The Back Bay Hilton is also very nice. I've always been treated well as a Hilton Diamond and (in previous years) as a Hilton Gold. The rooms are a bit small, but the corner rooms are a reasonable size (although the shape is a bit odd).
I would stay away from any of the airport hotels, as it is not very convenient to get into downtown Boston. You either have to take a taxi (about $20 each way), or take a shuttle to the T (blue line). In either case, it will probably take you 20-30 minutes (more if traffic is bad) getting to/from the hotel. I usually only stay at one of the airport hotels if I have an early morning flight out or am coming in on a late flight.