Both these sites are used (they cover the whole of Japan)

http://www.hyperdia.com

http://www.jorudan.co.jp/english/norikae/

Remember in Tokyo, there are more then just "subways" you have surface private railways like the JR Yamanote and Chuo, Chuo-Sobu Lines that can get you around Tokyo as well.

The above websites cover all the lines, subways, JR, monorail, etc.

Googlemaps is also a good tool if you want to figure out what stations might be close to the area you want to go to (along with guide books, japan-guide.com etc). An area can sometimes be serviced by many railway stations.

Additional information:
http://www.flyertalk.com/forum/japan...er-thread.html

Also I recommend getting a Suica or Pasmo card (covered in the previous post) which is a prepaid card, like a NY MetroCard but in IC contactless card format. Load it up, pay as you go, can be used on virtually every train company in the Tokyo area (and sometimes beyond to other regions of Japan).