It would depend on when you were landing back down, as I presume the boat will be swaying when you jump. So if you were hitting the deck when the boat was at it's peak (as far as your concerned) you'll be applying a forward and downward force on the boat, but if you hit when the boat is at a trough of it's ossilations, then this would cause the boat to go backwards as you would be applying a backwards/downwards force.
If you were just jumping up and down at random periods of time, I would presume that you would have on average as many jumps with a hint of backwards force as you do forwards and you would simply stay relativley still until you jumped out the boat through clumsyness.
Though my intuition says you would move a new backwards. :P