One of the places Miyazaki repotedly based Spirited Away on was the Edo-Tokyo Openair Architectural Museum:
http://www.tatemonoen.jp/
They don't seem to have an English website - but I'm sure if you google you will find plenty of information about it. It's in Koganei park, a little bit out of central Tokyo, but not hard to get to. It's a very interesting museum anyway - lots of old buildings have been moved from other parts of Tokyo, and rebuilt there in the park.