Generally you want to drive your boat up onto land (you can hoe a flat spot if needed) and take your axe to the mast and bust it back into its materials. Stow that in a chest at the workbench until you need it again, and build it on demand. This is also how you portage the ship across land, and you can also go through portals this way to build the boat on the other end.
Get used to breaking up your boat, in other words.
also, after the raft, boats are made with large numbers of *nails* which *sink* in the water. It is, at that point, critical to always park in viking deep or less water so you can recover the nails when the inevitable happens.
People (me too!) build elaborate docks and ports and such, which by the way you can do with little more than a hoe and wood. There are merits to this at your main home if it has sea access and you like having the boat around for effect. That is fine, it just takes some understanding of the key points above (that you will still need to bust and build if you use portals and that you need to park in shallow water). What I do is raise terrain with the hoe until I have a large (about the size of those A frame homes you find everywhere) area that I can walk neck/chest deep in when the water is calm (swim when big waves come in). Then I raise a terrain wall from the shore out so you can park along side this and jump back and forth from the boat. Taper it off or add a ladder so you can get out of the water if you take a swim. Then add whatever buildings you need to that.

a pic of one of my early goes at the above concept; this one is not quite big enough for the biggest ship but I mostly use the middle ship anyway. The idea is easy to see. I clearly have stone working at this point but that is just cosmetics.
https://steamcommunity.com/sharedfiles/filedetails/?id=2413829330