Think of a JR Pass as being a tool for traveling between cities. While it does work within Tokyo it's not the right tool to use.
If you're traveling between a lot of cities then the JR Pass is a good deal. If you're only traveling once or twice then it's not so great. Typically flying across Japan is cheaper than the train. The train is very convenient since it doesn't involve security and boarding lines.
For getting around Tokyo get a SUICA or PASMO card. These cost 500 yen and are your ticket to move anywhere within the city and also are accepted in a lot of stores that don't take credit cards. You can preload them with yen or tie it to a digital wallet. The metro system in Tokyo is arguably the best in the world and Google Maps works very well for navigating the city. You can buy one of these IC cards at any station.
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