it depends on what kind of nightspots you are going to
since you indicated that you would like to walk back from the clubs I'm going to just tell you which ones are in walking distance of the clubs I've gone to:

if you are going to clubs on lansdowne street (Axis, Avalon etc..), you can try staying at the Buckminster Hotel, Main Phone: 617-236-7050

if you are going to the clubs in "The Alley" (Pravda, La Boom etc..) you could stay at the new Hyatt Regency Boston which is about 2 blocks from there, Tel: 617-912-1234

If you are going to the Roxy, the closest good hotel is Doubletree Hotel Boston, Phone: (617) 956-7900

also I have a personal recommendation, if you are looking for a really quaint very nice bed & breakfast on Newbury street right in the heart of everything go to The Newbury Guesthouse(http://newburyguesthouse.com), it's beautiful and the staff is amazing.