Even easier, just spoof the GPS signals with your own higher powered broadcast and make the ship think it's sailing around while it's actually stationary. Cant find the link but, some university actually demoed this working in real life with an actual container ship.

Im imagining an LED throwie type big magnetic thing with gps RX and TX, and a satellite uplink. Cruise by the autonomous ship on a jetski near a port, thrown the magnet thing on, jetski away, disrupt from afar once the boat is out at sea.