Is it okay to retract your baby boy's genitalia during cleaning time?

By retracting your son's genitalia, do you mean to pull back his foreskin? If so, best no to do it as you might not be able to slide it back. As a baby, the head of his penis will self-clean to some extent. Pulling back or retracting the foreskin may cause it to tear where it is naturally attached, which can hurt your baby and leave scarring. This can also be the root of other problems for your baby boy later on in life.

Our first pedia advised us to retract penis everyday and clean with warm water and cotton balls. However, I've researched before that retracting isn't really good for baby boys so I stopped.

Do not do that as there is no need for that. When you give bath, it gets cleaned to some extent. And the skin inside it so tender that cleaning and touching it may cause rashes.

Please don't do that! My pediatrician had asked not to do so! The usual bathing cleans it.