Chomsky is by no means a saint, but in the wikipedia article you cited, I could not locate any direct "denial" of genocide done by Khmer Rouge. He seems to have questioned the credibility of certain accounts, which seems a necessary role of any reasonable intellect. It was 1970s, so information from the other side of the globe was harder to confirm. To me, it seems quite understandable for someone to raise questions around any information that outrageously deviates from the norm, which is the case for the activity done by Khmer Rouge.