never cruised in Asia. pretty sure the terminal is in the southeast area of Tokyo metro, near Haneda. We'll be around there this summer. Japan has maybe the best train system in the world, so obvious option #1 is get from the cruise terminal to the local train line, which I think is Rinkai line. Take Rinkai to a major station where the shinkansen train stops, prob either Shinagawa or Shimbashi, (probably not Tokyo eki as that is further away I think). from either of those 2 hrs by shinkansen to Kyoto.
Option 2: get ot Haneda by either cab or luxury bus and then fly to Kyoto. Now, little known fact. If you have FF miles to burn, domestic Japanese flights are super cheap when using FF miles. UAL & AA have relationships with JAL & ANA. I forget which/which. My wife handles that. So, get yourself from the Cruise Terminal to HAneda, Tokyo's smaller, closer in airport. Maybe cab. Maybe luxury bus. The luxury buses from airports to city center & between airports in Japan are awesome. There must be one from the Cruise to Haneda. The only reason there wouldn't be one is if it is a very short distance, in which case a cab is easy. I took the luxury bus from Kyoto's airport to downtown in 2022. Easy, not expensive.
and as I said, if you use FF miles and get any kind of good deal, option 2 may be both faster and less expensive. # of transfers prob the same since by using shinkansen you have to get into Toyo but end up in Kyoto city center. If flying, you prob get to Haneda in 1 move but you end up outside town in Kyoto (called Kansai airport). iirc, the bus back into Kyoto took 75 min or so? Kansai airport is actually closer to Osaka. the bus cost about $15 for the 75 min ride iirc
Wait, is there a small domestic airport close to Kyoto that planes from Haneda can reach? Not sure. Worth checking.
There is also obviously a train from Kansai airport to downtown Kyoto. Bus or train decision may just depend on arrival time and train vs bus departure time.