In Lord of the Flies, do Ralph and Piggy together symbolize the ego, or is Piggy the superego and Ralph the ego? Those who have made the argument that the boys represent Freud's theory of...

This wold make an interesting discussion point as obviously it is open to interpretation.

Golding always intended for people to view this novel philosophically and recognize the symbolism in each character. The superego by definition includes the conscience and all society's 'shoulds' and 'should-nots.' It is highly demanding and needs the influence of the ego to allow it to successfully incorporate into one person.

Lord of the Flies is  

an attempt to trace the defects of society back to the defects of human nature

and therefore it would not be possible for one perfect person, on the island to fit effortlessly into the novel. This is why Golding needed various characters - non less the personification of Id - Jack and his tribe - to present the complete picture.

Simon would definitely fit the definition of the superego; his friendship with Ralph and Piggy further cements this belief. His very spiritual nature, intuition but lack of social skills fits in with their practical positions and applications - hence the 'ego' as put forward by Freud. Piggy is the ultimate figure of reason and, as you say, complements Ralph perfectly in the composition of leader - neither would be effective as leader without the other.

Simon's ability to unlock the mystery of the 'Beast' and his death coming shortly after his realization further indicate a psycho-analytical approach. He is killed by Jack's tribe - the embodiement of that part of the personality called 'Id.'  The irony of the boys mistaking Simon for the "Beast" is unmistakeable.

Only the beast lay still, a few yards from the sea. Even in the rain they could see how small a beast it was; and already its blood was staining the sand.

The misinterpretation of Piggy as the superego (obviously a subjective view) could stem from the fact that Piggy does try to follow the rules and do what's right but it is more out of a sense of duty and what he believes his "auntie" would expect of him rather than his OWN value system. He too is swept away by Jack and wants to "taste the meat." Piggy knows when to retreat and urges Ralph

..There's going to be trouble. And we've had our meat.

Piggy's role does therefore respond to his more basic needs. The eNotes study guide and navigated pages will reveal more about Golding and the 'story' behind the story.