Most likely it'll be very cold at sea too, particularly if you venture outside. There's not a great deal to see on the route, I'd prefer the short (albeit probably more expensive) flight.
Thank You for your replies. Much Appreciated.Edited: 8:17 am, October 15, 2018
The only ferry is likely to be Blue Star at 15:30. Sunset is around 17:00 on 8th Dec, so you will do most of the trip in the dark. You will be able to see the caldera villages as you depart Santorini, and sunset from the ship if it isn't cloudy. I would take a flight.