Tokyo is served by the port of Yokohama, but isn't a cruise port. In total, Yokohama is the embarkation for over one hundred and twenty cruises every year from Cunard, Holland America, MSC and more to Asia, along with other places.
Cruises leaving from Tokyo during the peak seasons of spring, summer, and fall are much more expensive than the the low season of winter. On average cruises from Tokyo are fairly expensive compared to other ports. Look at the illustration below for the average cost per day by month.