I recently graduated from the Cooperstown Graduate Program, and thought I
would weigh in with my two cents.  As others have said, each program has
its advantages, and it is important to find one that matches what you are
looking for.
Cooperstown gives a broad overview of all aspects of museums -
administration, educational programming, collections management,
exhibitions, etc, plus museum-oriented academic courses.  Since
Cooperstown is such an isolated hamlet (I imagine there's about 3 feet of
snow there right now), and all your courses are just with other
museum studies students, it's a real immersion in museums.

Good Luck,