The THREE main ones are Tokyo Narita, Tokyo Haneda, and Osaka KIX airports.
If your cruise ends at one of the 6 Tokyo Area Cruise Terminals, Tokyo Haneda is closer to all of them.
If your cruise ends at Kobe, you will be at either Naka Terminal or Kobe Terminal. The nearest large International Airport will be KIX Osaka.
If your cruise ends at Osaka, it will most likely be at Tempozan Terminal. KIX Osaka Airport will also be your best choice.