Hi UFO. The best theatre organ in Amsterdam is in the City Theater, but if I remember correctly, around when you will be there, they will be deep in rehearsals for end-of-summer productions. They have recitals very infrequently as it is. The theater doesn't list an email address on their newsletter, but you could call the offices at +31 (0)20 523 77 00 (they're pretty friendly), and they could refer you to someone in charge of the organ (I haven't tried myself). The Pathé Tuschinski has a Wurlitzer, which has stood the test of time pretty well, but they run movies pretty much continuously (it's an active movie theater). If you get a chance, though, you should see a movie there; absolutely gorgeous building. The most high profile recitals during the summer are at the Oude Kerk, which has a fantastic organ, albeit very baroque. I'm not as familiar with the organs outside of Amsterdam, but there's a little Compton in Middleburg, Holland, with a nice big sound, which is getting old, but not too cranky. I can't find any contact info, though.
Best of luck.