My neighbor installed a car alarm on his, with motion detectors. I've been known to "nudge" his "Boo" on ocassion, just to screw with him. He got micro switches for the trunk and storage compartment. You could also put one on the radio so if it were slide out from it's cradle, would set off the alarm.
Maybe you could try motion detector lights on the boat lift. We have sporatic larcenys by dirtbags in boats at night, so I can sympathize with you're plight.