The last shinkansen from Tokyo to Kyoto is at 9:20pm. They could, if they wanted to, go to Kyoto on their arrival date. The last Hikari shinkansen (on which the JR pass is valid) is at 8:03pm. They could catch this too unless the plane was significantly late.

It's a long trip but the shinkansen is comfortable, it will be dark outside, and they could nap on the train.

There is no rail pass which includes the fastest (Nozomi) shinkansen between Tokyo and Kyoto. Note that when it is travelling, the Hikari shinkansen goes just as fast as the Nozomi, the reason it's slower is because it makes one or two more stops.