I see some "holes" in your plan.
1. If you saw the door to your boat ajar, and climb up to look inside you would be silhouetted against the doorway, making you a much better target than the perp inside.
2. The perp could have explosives and blow you both up.
3. If you killed him, it would be very difficult to interrogate hun about others who may have been involved.
4. In view of #3 you might very well be prosecuted since your life was not in immediate danger, and you could have simply notified the zillions of cops in the area.
You missed the part about my “throw away”.