Whenever I have a stowaway, first I ask them nicely to get off of my ship. If (and usually when) they don't listen, I yell at them and threaten to report them. Sometimes, even that doesn't work, so I get a friend to come follow me and challenge them to PvP. Works every time, especially because they're n00bs who think they can take out a level 30+
I refuse to let these "leeches" gain any gold from MY work when sailing, so that's why PvP is the best option for me ^^