I tend to use a hoe or an ancient tree as a spot to dock my boat and usually whenever I do use a boat I will destroy it once my resources are safe and then immediately set up a portal and stow away said boat in a chest just in case I need it.

I recently relocated to another plains area and use the hoe to make a decent landing spot + road for cart use to move all the metals. Then I destroyed the long ship since I didn't need it anymore.

edit: I have used stone for wharves before as that is a bit more resilient then just wood.