Checked the 3D map of Japan yet?
This 3D map might not be the best. Google earth is probably much better but its is very simply organized and very easy to use.
This page is in Japanese but you'll probably have no problem using.
It is that much simple.
I recommend this map system.
Aries Home Page
http://www.asahi-net.or.jp/~XJ6T-TKD/
Aries Home Page 3D map of Japan
http://www.asahi-net.or.jp/~hw3t-tkd/bou2/bou2all.html
