Phase 1: Hand Attacks
Bongo Bongo is an invisible beast with two hands that attack you on a giant drum. Use your Hover Boots to stay on the drum. Target one of his hands with Z-Targeting and shoot it with an arrow or hit it with your Hookshot/Longshot. Repeat for the other hand. This will stun his hands.
Phase 2: Eye Attack
Once both hands are stunned, Bongo Bongo will reveal his giant eye. Use your Fairy Bow to shoot his eye. He will then charge at you. Attack his eye with your Master Sword. Repeat the process, avoiding his hand slams and the toxic liquid surrounding the drum. Keep your distance and use ranged attacks effectively.