YCAT

Hi Kaori-san!

Unfortunately you can't use the JR Pass for the YCAT bus to Yokohama.
However you can take the Narita express to Yokohama .
It will bring you there in style good time.

http://www.jreast.co.jp/e/routemaps/index.html

You can't use your JR Pass for the Tokyo metro but you can take the JR Lines in Tokyo such as the Yamanote line that makes a circle trough Tokyo and hails at many of the important stops.

Feel free to ask more questions if you need more help.
Daniel

For reference, here's another map of JR lines in Tokyo for you to use when planning your trip.

Hope this helps!