Which JR pass + Tokyo subway system

Hello we have an 18 day trip to Japan next month wherein we land in Tokyo (Haneda) mid-March and stay 1 night before travelling by train across Osaka/Kyoto/Hiroshima for about 11 days, before returning to spend our final week in Tokyo.

My question is whether Tokyo alone is worth having a JR Pass, or whether it is easily navigable by the Subway system (which I believe is exempt for the JR Pass). Because currently I am thinking to use a 14-day pass for the main leg of our trip around the country, and then just rely on standard subway/train fares for the final week in Tokyo... however if it's worth paying extra and using the 21 day pass for Tokyo too, please let me know?

Thanks