October in Japan is going to be a lot like October in Europe and America, namely autumn. In Tokyo, expect daytime highs around 20°C, mostly clear skies but occasional rain, beautiful autumn foliage.
Personally, late September/early October is one of my favorite seasons to be in Japan, second only to cherry blossom season around April. Not too hot, not too cold, and off-peak so not too many tourists. But if you're expecting beach weather, then sorry, you'll only find that at the southernmost tip around Okinawa... and since Japan is a long and skinny country, there might already be a dusting of snow up in northern Hokkaido.
There's one catch though: October is the tail end of typhoon season in Japan, which could make a cruise pretty unpleasant (and explains the high precipitation readings on the chart linked to above). However, the peak is Aug-Sep and the typhoons usually hit the Pacific side of the islands, not the Japan Sea side you'll presumably be sailing on, so odds are pretty high you'll be OK.