The only "museum" of that kind in Amsterdam would be Perlee's
collection ( http://www.gperlee.com/museum.html ), though
I understand that it is currently closed for renovation.
All the organs in that collection are currently stationed in
the National Museum "Van Speelklok tot Pierement" in Utrecht.

There should also be an organ in the Stedelijk Museum, which is
known as the Busy Drone: http://nl.youtube.com/watch?v=UMDN4xE_CjQ

and http://nl.youtube.com/watch?v=WZiOFAs4GKs
  Should you run into
it there, it will probably only play the "music" you hear in the
second video, if it plays at all.

Also, as the 10th of May is a Saturday, there should be several
organs playing, too, spread throughout the city (around the
Kalverstraat probably).

Hope to have helped,
Thijs Haenen