For one day in Tokyo there is a great post that shows some of the most famous places to visit on this website:
The JR pass is only valid on JR trains, but in Tokyo there are many more railway operators. To access all the places you want to go you might want to consider getting a Pasmo/Suica card which you can purchase from a ticket vending machine at any train station for a refundable 500 yen. The card can then be charged with money that you can use all throughout Japan, including Kyoto, to travel by bus or train simply by touching the card to the card reader area on ticket gates and buses. The card can also be used when paying at convienence stores etc.
Hope this can help you and have a nice trip!