I am not really into that and my advise might therefore not be relevant, but here are some hints TBC:
- there is a site in Nikkou (rather surprising, I know), somewhere on the left of the road going from the temple to Chuusenjiko. A friend living in the area visited the place and found it amazing. Sorry if it is a bit vague, but you should be able to find it on a map,
- the sea side part of the Kawasaki area is very industrial, and you might find some sites there, but chances are that new stuff were rebuilt in most locations. Japanese rarely leave any space un-used for long around Tokyo...
- Gunkanjima near Hiroshima (far from Tokyo though) has potential but its access is seemingly forbidden nowadays,
Japanese colleagues I asked were unable to provide any hint besides these.