JR Pass usage

Hi there,

Hanzomon is a Tokyo Metro station on the Hanzomon line and not a JR Pass, there is a convenient JR station closeby called Yotsuya Station. From here you can get on the JR Yamanote line to Tokyo station, from where you can use the bullet train to cities like Kyoto and Yokohama (for the cruise terminal).

For Fuji, please see:
https://www.jrpass.com/blog/itinerary-tip-mt-fuji

Hope this helps,
Daniel

which JR train should I take to go to Yokohama cruise terminal from Tokyo station?

The Station is called Nihon-Odori, take the JR Yokohama line from Tokyo to Yokohama, then take the Minato-Mirai line to Nihon-Odori Station.