He can be tough but once you know how he works he's very easy to defeat. The main focus should be on his hands. Try not to focus on one hand too much otherwise you don't see his other hand attacking you. The best thing is to shoot as fast as you can one hand so you only have the other hand to pay attention to. Just get your bow ready or the hookshot and shoot it as soon as you get the chance. Then use the lens of truth to shoot his eye. And beat him up.
Repeat the whole thing. He is possibly the most difficult boss in the game because of his hands but once you've beaten him it's more easy to beat him next time you play OoT.
Maybe other members have more easy eays to eat him but it's all about timing
Vanessa28's advice is spot on. What makes it hard is the speed the other hand moves once you stun one so you just need to act quickly. If using the lens of truth to see the eye is adding another layer of complexity, know that you don't need to use it. Bongo Bongo's eye is always in between the two hands when he charges after both hands are stunned so aiming for the middle with the bow or hookshot will work.
Also a little known trick is that the ice arrows actually are useful in this fight. You only need to hit one hand with an ice arrow to be able to stun the eye rather than hit both hands with regular arrows. However, obtaining the ice arrows is harder for most people than beating Bongo Bongo so this is almost useless.