The law of conservation of momentum tells us that the sum of momenta before the collision is equal to the sum of momenta after the collision. The bag has no momentum as it falls onto the boat because its velocity is zero in the horizontal direction. But after it hits the boat, it's momentum increases while the momentum of the system remains the same. That means a component of the system must decrease somewhere else. And that component is the velocity, not the mass, of the boat.
