I assume your cruise ship will be at Tempozan port.

KIX to Tempozan = Bus ride (70 mins)
ITM to Tempozan = Bus ride (40 mins)

Flights from NRT to ITM all seem to be between 3.40pm and 6.00pm.
(Not ideal for you)

There are currently no flights from NRT to KIX

There are lots of flights from HND (Tokyo's domestic airport) to ITM and to KIX

If you enter Japan at NRT, you will need to take all your luggage through Japanese customs at NRT. Not possible to check it all the way thru.

If you strongly prefer to travel by plane, then I think your best plan is to take a bus from NRT to HND. Stay at the airport hotel in HND. Fly the next day to ITM or KIX. Then take a bus to Tempozan.

EDITED TO ADD:
Or - Take a bus from NRT to HND. Then a late flight to ITM or KIX. Stay at ITM or KIX. Then bus in the morning to Tempozan.

With all those buses and a plane, it's quite an effort. I don't think the train would be significantly harder.

I suggest that you ask a moderator to move this to the Tokyo Forum, where you will get advice from folks who know the area well.