I was going to suggest having a separate dock that you can build and place, but I like the idea of giving shipyards another use. I think you should be able to pull a ship near a shipyard, access your ship, and then select to dock. At that point your boat appears docked and anchored with an easy way on and off, like the scaffolding while you're building a ship.
Also, shipyards should be more forgiving to place.