Good question, I never really played with Unreal, I don't think it was free when I started all of this. I think Unity had a free version, but it was very limited. I actually started out using a game engine called Torque 3D, but struggled quite a bit with it.
I started messing with Unity in 2016 after playing Design It Drive It Speedboats made in Unity by Todd Wasson. I found that Unity's Asset Store made it really easy to get started. At the time the water assets for Unity were much better. I'm not sure if this is the case anymore, but at this point I don't think switching engines is an option.
I'm pretty sure that both Unreal and Unity use the NVIDIA PhysX engine for physics, so there isn't really a difference there. All the boat physics is custom code calculating forces that just feed into the physics engine.