My Wife and I stayed at The Inn at Union Square". We loved it so much we went back three times since then. We stayed in The Penthouse on our Honeymoon in a two day layiver going to Hawaii. We have since stayed in two of the graded rooms and they are very nice as well.
Depending on when you are going you may not get a room. If I remember right we had to book well in advance.
I have told many people about his place over the last twenty years and no one has come back and said they were not more than pleased with the prices, rroms and service. It is a small quaint place just off the Square.
http://www.unionsquare.com/