How old will the three children be when they travel?
[Shinagawa Sta. / Tokyo Sta.]
Shinagawa is much better than Tokyo for a transfer between a "Narita Express" train and a Tokaido Shinkansen train.
In Tokyo, "Narita Express" trains use tracks deep under the ground while Shinkansen tracks are above the ground. (HyperDia indicates the former tracks just as "tarck No. 3" and "track No. 4"; however, actually they are not Tracks 3 and 4 on the ground but Sobu Underground Tracks 3 and 4.)
And, in Tokyo, JR-East and JR-Central have Shinkansen zones separately, which are located nearby.
In Shinagawa, non-Shinkansen tracks (of JR-East) and Shinkansen tracks (of JR-Central) are on the same level. You can make a transfer to/from Tokaido Shinkansen via one of the two passenger bridges, passing through either Shinkansen North or Shinkansen South Transfer Gate.
And, JR-Central is the only JR company which operates Shinkansen in Shinagawa.
- Map of Shinagawa Sta. (of JR)
http://english.jr-central.co.jp/info/station/_img/shinagawa_L.jpg?unti...[Shin-Osaka Sta.]
To Osaka Station, Shin-Osaka Station is much closer than Kyoto Station.
- Map of Shin-Osaka Sta.
http://english.jr-central.co.jp/info/station/_img/shin_osaka_L.jpg?unt...In Shin-Osaka, you can go down from the Shinkansen platform to the concourse, pass through Shinkansen Transfer Gate, walk a little and go further down to the platform for Tracks 15 and 16. Then you can take any train departing at any of the two tracks to Osaka Station, which should be the next stop.
[Narita Airport Sta. / Airport Terminal Sta.]
Please note that Narita Station is located outside the airport.
JR-East and Keisei have stations in the two terminals of NRT.
"Narita Express" is a Ltd. Express service of JR-East.