Tokyo to Kyoto then travel around Tokyo

I'm spending a week in Japan, arriving in HND then travelling direct to Kyoto from Shinagawa. Then after 3 days back to Tokyo for 3 days and finally flying out of NRT.
Is it best for me to by a JR pass, which I can use on the Hikari to/from Kyoto but also on trains around Tokyo? This will also take care of their airport trips too.
I assume I'll also need to buy a Tokyo 3 day underground pass, which I understand I can buy at HND but won't actually use until I return to Tokyo.
Am I doing the right thing? Hope someone can help. Thanks, Roland

You might break even with a 7-day JR Pass, and if you buy one you don't need a subway pass in Tokyo (because you can get around most of Tokyo with JR trains, which is covered by the JR Pass). To maximize the usage of JR Pass, you can ride the monorail from Haneda airport to Hamamatsucho, transfer onto a Yamanote Line train to Shinagawa or Tokyo station, and get on a Shinkansen (all rides are covered by the JR Pass). In Kyoto, a JR Pass is not much useful (except to go to the Arashiyama Bamboo Grove and Fushimi Inari Shrine). For the trip to Narita airport, ride the Narita Express (N'EX) which is covered by the JR Pass.