When exploring I find a large offshore rock. I 'anchor' swimming distance from that rock. I then swim to the rock, then from rock to shore. I mark my boat location on the map. To be safe I put a campfire on the shore closest to rock/boat. I also never make landfall in the swamp or plains biome.

For a base there are countless ways to dock your boat.

https://steamcommunity.com/sharedfiles/filedetails/?id=2502632638

https://steamcommunity.com/sharedfiles/filedetails/?id=2581488414