I've been looking for something like this for a couple of years now, stumbled onto this while looking for something else entirely:

http://japonyol.net/editor/railway.html

I can't vouch for accuracy, but it seems to be pretty good for what I've looked at so far. I do note that it only shows NEX to Tokyo and not the other branches. Also, you can only view one line at a time - the option to view all subway lines leads to a 404 error.

While schematic maps are great, this will show you where the lines run geographically.