Vire has 3 attacks. He's difficult to hit with your sword unless he does his yellow ball attack, which becomes less common as the fight goes on. When he's circling you, he can be hit with a well-timed bomb.
Hit his face with the seed shooter when he's turned away. Then charge up a spin attack and hit him when he turns around. Eventually he'll go underwater, where you can either slash him with the sword or punch him with the expert's ring.
Sometimes this boss will disappear when you go above water. Keep going below and above water, and he will (hopefully) reappear.