Is there such a thing anywhere? Search turned up nothing. I'm assuming kaiju is represented in some larger scope toy museum, somewhere. Most likely in Japan.
The Kodomo no Jidaikan museum in Niigata (Yuji Nishimura's place) is open occasionally, mostly holidays. During my first trip to Japan there was a Godzilla exhibit in Odaiba. They had costumes from the 2002 movie on display, pretty beat.
There is also the Ultraman Festival every August in Ikebukuro. Usually they have some mixture of toys, props and costumes. Some years are better than others. There is always a theme: 2006 - 40th anniversary of Ultraman 2007 - 40th anniversary of Seven 2008 - Spaceships of the ultra series 2009 - Robots. Not sure whats the theme for this year. Its the 30th anniversary of Ultraman 80. Starting from next year the 40th anniversaries of the Silver Age Ultramen kick off (71 - returns, 72 - ace, 73 -taro, 74- leo)
Not dedicated, but somewhat related... Over the summer at Epcot, the Japan Pavilion was hosting part of the collection from "the" Japanese tin toy king. Unfortunately, I had left my camera in the car. Dumb Dumb Dumb
that exhibit had been on display for a very long time. There were more toys when it opened a few years ago and the show dwindled down until it finally closed.
If you mean Kitahara you can see a small percentage of his collection (still a ton) at his Yokohama Tin Toy Museum. From my understanding he also has several warehouses housing his full collection which are not open to the general public. Madness!