Takuhaibin or 'takkyubin' is the name for luggage delivery service.
Basic introduction to takuhaibin, door-to-door delivery services in Japan.
www.japan-guide.com
I don't know of any specific places in Yokohama ( assuming that's your cruise port), but most hotels will handle luggage shipping to another hotel. The link above says takyuubin service is available at major rail stations. Also some convenience stores offer it too. The Yokohama station is very large and has several levels & entrances, so you'll need to research or ask at your pre-cruise hotel or maybe a taxi driver after cruise?
Be sure to have the destination hotel send you their name and address written out in Japanese characters. (I had ours in English and got a look of scorn from the hotel bell hop who was filling out the delivery form for us. )
If you're taking the train, I saw online that some now offer specific seat reservations for 'oversize' luggage...I suppose seats right next to a luggage storage area in the back of train cars.
I:m also guessing for a train from Yokohama to Kyoto, that you might have to switch trains at Osaka.
Good luck.