What's wrong with leaving him down below??
A mattress on the floor between the settee and the table makes a great cot and most 13-month old's I know aren't at the climbing stage (yet!), and could never climb out of the cabin or get up on a berth whilst the boat is moving - the sides are too steep - particularly when wearing a WeeWilco.
The motion of the boat (the "moving floor") will be something he's never experienced before and will either have him in wonder for the entire trip or rocked fast asleep.