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The Official Museum Directory (yearly editions) 
The Official Museum Directory is published through the American Association of Museums.  It's heavy -- in weight (5 pounds), in price (over $300) and in tone, and has more than the casual reader probably needs.  But it is the largest collection of really detailed information around. Buy it through Amazon,

Special Museums of the Northeast 1985 Nancy Frazier ISBN:0871068699
Older, but written by someone who has been to each place she describes.  Check other sources (like our Resource Guide) for current  hours, phones, etc. Not all the 144 museums are obscure or super-specialized, but the writing gives a good "feel" for each. 

Art Lover's Travel Guide to American Museums 2001 2001 Judith Swirsky ISBN:0789206897
Brief descriptions of the museums, contact (including web sites), types of materials in the collections, and even special exhibits for 2001 in some cases.  Buy the latest version, if only for the URLs.

Children's Museums An American Guidebook 1998 Joann Norris ISBN:0786404434
State-by-State, a couple of paragraphs on each museum, hours, fees, contact info