They are seen near the beginning of the film, making the opening of the fishing season in New York City.
Near the end of the film, after the final battle with the sharks, The fishermen appears and tried to catch the fish by using a huge net. Derek, Little Alan and Nellie Pinky tell the fish to swim down. They were defeated when the fish escape, and causing the boat to tip over, and then the net finally breaks. It is unknown what happened to them afterwards, but they are presumably arrested for several crimes.