I have seen a few mashups with Google maps that show stations in their locations on a street map. We had a discussion about one on this forum, when it was in Beta mode. I'm not sure if this is the one:
http://campo-salado.com/railway.html

As for ease of connection, there are some guidebooks that you can find in railway station book stores. They typically show the easiest connections, locations of restrooms, and whatnot for all the stations. Apps like navitime will allow you to select routes that minimize walking distance or stairs etc.

At the very least, I recommend that you get familiar with the train diagram posters that are posted on the pillars on subway station platforms. These plans will tell you which car to travel in for easy access to the exit at your destination. If there are multiple exits at your destination, it will detail which ones have elevators/escalators/stairs etc. and which ones are most suitable for the major sites around the station. Not bad.

BTW - You're lucky if there's "one" map that you're always seeing of the system in Tokyo. Sometimes it can be a challenge to reconcile the map in your hand with the spaghetti that you see on the wall.