Short casting from the seat of your ship is the key. Reel in until the bait is just in the water, the fish will bite just the same. When they do, stand up and pick the fish directly off the line without reeling in. You can catch multiple fish with a single piece of bait this way.
Disappointing they nerfed the leaping fish as every now and then one would jump right into my ship. With good reflexes you could even grab them directly out of the air.