On a water world, everything of importance could be under water instead of on top of it. This means you can convert your whole navy into submarines where they can better access and control these under water territories. Your ocean can still have an atmosphere above it where planes could fly, and planes would still be an important technology because they can travel so much faster than submarines, but they would have very limited means to interact with what is happening below the waves. Because airplanes can't see what is under the waves without some kind of sonar device in the water to transmit them information, they would be flying blind more often than not. In fact, the fleets could be so deep that airplanes may not have a good way to engage them even if they did know where they are.
The advantage of ships would be further enhanced if we are talking about an aquatic species instead of humans. Their airplanes will need to carry a lot of water so the pilots can survive out of the ocean. Putting just a single cubic meter of water onboard to fill a small cockpit would add an entire metric ton of weight. That is the weight of the entire explosive payload of many WWII era light bombers; so, meeting the engineering needs of both breathing out of water, and packing weapons that could sink a ship would be much harder.
IMPORTANT EDIT: Forgot to specify the more basic assumption: The boats
and planes are being built by a land-dwelling species, so along with
air and sea, the planet must have dry land.
Well this edit derails my original answer... so here is another option along the same vein of thought that should still satisfy your needs. Make the atmosphere much thicker than Earth so that it is LIKE moving in water. Airplanes experience drag in proportion to lift; so, on a planet with a much thicker atmosphere, planes would still fly just fine but much slower. Instead of being able to move in at hundreds-to-thousands of miles per hour, planes would be restricted to speeds that are not much better than ships in the sea, or cars on land.
By taking away their mobility advantage, they would be much easier to pick off with AA weapons, and much harder to deploy when and where you need them. Deployment ranges would be drastically nerfed as well since it would take more fuel and time to cover any given distance.
Apart from slowing planes down, it would also make them more maneuverable. This would make interceptors far more effective such that fighters escorting your fleet could more effectively intercept inbound bombers before they can reach their mark.
The last and perhaps most important point about planes is engagement ranges. In general, larger weapons platforms can support longer ranged weapons. In the current model of air superiority, planes often have less range than ships, but they can use their speed to close into their own kill range very quickly. In contrast, if planes were much slower, then they would have to spend a lot longer between coming into the range of the ship's heavy cannons/ long-range-missiles and being in range to launch their own much smaller, more range limited torpedoes.
Perhaps a better way to visualize this is to picture any modern conflict between a naval bombardment and tanks. Tanks should be able to harm a warship if it could get close enough to shoot back, but in general it can't so the tanks just get wiped out.