You need one of these in your inventory,
http://wiki.cantr.net/index.php/Category:Writing_items , then click on the name from outside it (so, if it's docking to a harbour, you'll need to be standing out there). Then you can start a project to give it a new name.
Lots of useful info on the wiki, and if you want to do a little digging, same on the forum.
All the best.