Greater Boston
The Computer Museum is now part of the Museum of Science.
DeCordova Musuem
The Discovery Museums
The Isabella Stewart Gardner Museum
Harvard Art Museum
Museum of Fine Arts
The Museum of Science, Boston
The New England Aquarium

Other
Museums of the World
Art Museums Network

Additional Internet links/pathfinders for this subject:

Librarian's Index to the Internet - Museum Topics

About.com (enter search term "museum")