I think a lot will depend on what you are trying to accomplish, or what challenge you are trying to present. If there is going to be fighting on the deck of the ship, then you want the map version. The docks really don't matter at that point, except for how far the PCs need to swim (or whatever) to get onto the ship, and how far it would be for them to swim (or whatever) if they need to retreat. At that point, it doesn't matter if the ship is moving, or if you are moving the dock farther away, because all that matters is the relative distance between ship and dock. Since you may be using dynamic lighting on the ship if there is fighting anywhere other than simply on the open deck, you may not really want to move the ship anyway, since that would mean you would have to move dynamic lighting lines also. If stopping the ship doesn't necessarily mean boarding that vessel, then the token would be all that would be needed, while the PCs are racing to engage some sort of harbor defense to keep it from leaving, or get other vessels to block the vessel's path. Are there allies of the fleeing vessel operating on land that will oppose what the PCs do? I have used Pickard's Quick Encounters: Ships Pack 1 for stuff like this. There are other sets with different styles of ships and boats, if you prefer a more obvious fantasy design. It has the water background that at least matches the overall color of what is around the ship illustrations. I use the tokens for long range maneuvers/attacks, and then switch to the more detailed layout when/if there will be melee combat. Sometimes I have used the same map page for both, simply dividing the map page with a dynamic lighting line.
