Brest hotel I've ever stayed at in Boston is the FS on the Common. I am surprised no one has ever mentioned it here in this thread. It's been a while since I stayed at the old RC but the FS is way better.
The Boston Harbor hotel rooms are decent, the service is nothing special, I would stay there when I have to attend a conference at the Marriott Long Wharf (which is hugely unimpressive).
Just stayed at the newly renoved Hyatt Financial District (formerly a Swissotel) and was not impressed with the renovations but it might be good value if it's coming up cheaply on Priceline.