It is dystopian. The boys end up fighting and some die; hardly an ideal of utopia.
The setting and circumstances are utopian; children living free of the impositions of adults on an idyllic tropical island. The fact that the boys crash on a desert island is meant to propose that it is utopian because they come from a world engaged in atomic war. (The corollary is WWII). The boys work together at the start but quickly devolve into fighting factions; all arguing over the rules and fighting over the means of survival; namely Piggy’s glasses.
Even utopian works can be interpreted as dystopian. Utopia is an ideal society (so ideal that it is hard to imagine). Fittingly, it means “no place.” The Lord of the Flies is on an island and this is a direct reference to Sir Thomas More’s Utopia which was set on an island. Ralph is a reference to Raphael in More’s book which may be a reference to the archangel Raphael. In Christianity, Raphael means ‘healer.” In Islam, he is responsible for signaling Judgment Day by blowing the horn (Sur) to send out a blast of Truth. This is a clear reference to the conch as the means of restoring order. This also illustrates that Ralph and Piggy in particular (The Lord of the Flies) are characters which expose the Truth that this is not a Utopian island. Both More’s and Golding’s books are satires since they metaphorically comment on their own historical context. The Lord of the Flies is certainly dystopian. And some might argue that More’s Utopia is also dystopian, certainly in historical hindsight because it endorses slavery, severe punishment for adultery, and euthanasia. So, even utopian ideas tend to be fraught with contradictions.
Other dystopian novels: Brave New World, 1984, Anthem, Animal Farm, A Clockwork Orange, The Giver.