Japan Rail Pass can be used on all JR lines in Tokyo, including Yamanote Line, Narita Express (N’EX), and Tokyo Monarail to Haneda Airport. Show your pass to JR staff at ticket gates, do not go through an automatic gate. Here is a full map of all JR lines in Tokyo area.
Japan Rail Pass cannot be used on other (non-JR, Odakyu, Keio, Toei) train lines or subways in Tokyo area.
See this article for details: http://www.japanstation.com/japan-rail-pass-discounted-travel-on-japan-railways/