Negative, I mis-read the google map result earlier.. If you want to go straight on JR without taxi, you can get off NEX at Tokyo Station platform 1 deep underground, then wait for the next train (normal slow train) at the platform 1 / 2 bounding Yokohama at get off at next station (Shinbashi), most of the walking is done by underground walk-way towards shiodome direction

http://local.google.com/maps?f=d&sou...,0.004823&z=18

With this you avoid the taxi hunting others may worry about.

I think the scenery train plus the river journey @ Kyoto should be interesting for kids ? http://www.sagano-kanko.co.jp/eng/index.htm

Or the deer @ Nara ? http://www.japan-guide.com/e/e4103.html