I'm using Osaka as a base. If you're flying into Narita, I'd look into shipping your luggage from Narita airport to your hotel in Osaka - it'll get there the next day and the cost is relatively reasonable. That'll allow you to take a train to Tokyo station and transfer to a bullet train to get to Osaka (trains are easily the best way to get around Japan) - approx 2-3 hours away.

As I commented in your other thread, Osaka-Kyoto are only about 1-2 hours away by train. Nara is also about the same distance away from both cities as well. Both Osaka and Kyoto would make a good base to explore the area from but since you need to transfer to the ship with luggage for embarkation, Osaka makes the most sense from my standpoint.

Masaki