Yes, you can use the JR Pass on the Yamanote line (Tokyo loop line that goes around Tokyo and serves most of the big stations), the Chuo/Sobu line (Runs accross the Yamanote loop line from East to West) and the Tokyo Monorail. You can also use the JR Pass on other JR Lines that go to the outskirts of Tokyo. If you are arriving at Narita Airport you can use the JR Pass on the Narita Express.