I don't think so, no. A utopia is a society in which everyone is happy, everything goes wonderfully, everything is fair - a dream world! A dystopia is the opposite: a society with awful conditions, usually ruled over by a strict regime, where everyone is miserable. And I don't think that "Lord of the Flies" is either a dystopia or a utopia.
Firstly, it's important to point out that, when talking about "Lord of the Flies" as a society, it's a sort of society, within a society. The boys crash to the island because their plane is shot down, the parachutist is shot out of the sky in his plane, and, at the end, they are rescued by a naval officer. A war is raging outside. We don't know the details of it - and certainly not enough to call it a dystopia - but the novel is set against a background of war.
Then there's the society on the island that the boys create. Ralph's equal society, though flawed, aims towards being a utopia with rescue as its main focus. Once Jack takes control, the boys' society veers toward utopia: Jack a tyrant, ruling unilaterally over the boys, and violence administered when Jack is disobeyed. Those last few chapters are as close to dystopia as the novel gets. But it's not a term I'd use to describe it - call it a "tyranny" if you like, or a sort of "sub-fascist regime".