Narita Express --> Tokaido Shinkansen --> Kyoto

I'm deciding whether to board the Tokaido Shinkansen (bound for Kyoto) at Tokyo Station or Shin-Yokohama Station. The Tokyo Station looks intimidating to navigate and I'll be traveling as a family of 4 with luggage.

Would the Shin-Yokohama Station be a better option? At this station, is the transfer from N'EX to Shinkansen straightforward? I'm looking at a late Thursday morning (11am) boarding time on the Shinkansen. Will I have a problem getting seats for 4 sitting together (with my JR Pass) at that time of the day?

Thanks!