When it comes to trains in Japan Hyperdia[1] is your ultimate friend.
It's the electronic time table for all things (train) travel in Japan. I put (train) in quotes because it also displays flights if the routing is more convenient.
Searches are highly configurable and it provides not only the best routing, but also includes the prices for the available options.
https://travel.stackexchange.com/questions/53640/where-can-i...
Unfortunately the pics of it are tiny, but as a sampler, here's what greater Tokyo looks like:
http://ontheworldmap.com/japan/city/tokyo/tokyo-rail-map.htm...