If this vessel poses such a threat, why not utilize maritime aircraft to locate it, and then sink it as a menace to navigation using either naval gunfire or a torpedo?
Find it, board it, place 3 batches of C4 (50 lbs each) at three locations inside the hull below the water line. Get the hell off and watch the fun when the C4 goes bang. This is much cheaper than using naval fire or torpedoes.