Thanks Everyone! Looks like Suica is the way to go.
My apologies for not being specific enough in our question. Initially upon arrival we are staying at Shin-Yokohama Prince, which sort of puts the NEX out of the picture.
We travel independently and make all our own travel and accommodation arrangements.
After a few days at SYP we go up to Tokyo for three days before heading south to Hiroshima for three days, stopping in Kyoto for three days on the way down. From Hiroshima we return to Yokohama, this time staying in Minato Mirai for about a week. At some stage we will break away for a couple of days (1 night) in Hakone.
Because we want to use the Nozomi we shall not be buying the Japan Rail Pass.
While in Yokohama we plan on revisiting some previous stops, including Kenchoji Gate and the nearby Giant Budda.
Although shopping in touristy areas like Ginza we often found more of the ''real'' world in places like Himonya Daiei, the arcade at Musashi Koyama and even the area around Senzoku.
ANY advice or suggestions would/will be appreciated.
Thank you again to everyone!