This paper presents a Model Predictive Control approach for autonomous landing of a quadcopter on the deck of a moving boat. The research is motivated by a large-scale demonstrator arena equipped with autonomous boats and drones that should collaborate to perform various tasks related to search and rescue missions. The landing maneuver is executed in a cooperative manner where both the boat and the drone take actions to reach their common objective. The maneuver is designed to be feasible under a range of conditions, including scenarios where the boat is moving across the water or when it is subjected to disturbances such as waves and winds. During the landing, the vehicles must also consider various safety constraints for landing safely and efficiently. The algorithms are implemented both in hardware-in-the-loop simulations, where we demonstrate some of the different scenarios that the algorithm is expected to handle, as well as on a real boat-drone system, on which initial tests have been carried out.