IMPORTANT DISAMBIGUATION. Whale sharks are widely advertised alongside Raja Ampat but they are not in Raja Ampat. The aggregation is in Cenderawasih Bay, roughly a three-day passage east, where the animals gather around fishing platforms (bagans) and are hand-fed by fishermen. Encoded 'absent' for Raja Ampat itself, and flagged as provisioned rather than natural. If whale sharks are the reason for the trip, you are booking the wrong itinerary.
The 'limited' case this field exists for. Nothing closes, but from roughly May to September the southern monsoon brings strong winds, high waves and visibility down to 10-15m, and a substantial share of the liveaboard fleet suspends Raja Ampat itineraries or repositions elsewhere in Indonesia. July and August are the worst of it. Resorts stay open and sheltered sites stay diveable, so you can still go, at lower prices, with fewer options and a real chance of blown-out days.
Destination detail