The irony of the natives
When the clumsy Europeans realize that living on an island calls for a very specific skill set that they don't have, they are suddenly very relieved to find natives that look very friendly, and who once spotting them are indeed very friendly. However, these natives have an ironic twist—they are murderous cannibals who are almost certainly fattening them up for a ceremonial slaughter.
The irony of willful ignorance
Let's be honest about Tommo. He knew they were cannibals, but they were nice to him, and the guys on the boat were mean. They gave him unimaginable privilege and spoiled treatment, and his romantic problems went away because there were plenty of foxy natives who were excited to be around him, naked and available for his every whim. The irony is that he knows they're cannibals basically from the beginning, but it takes the actual encounter with cannibalism for his body to appreciate the severity of the situation. Ironically, he had willfully compromised his own safety to gain a little bit of pleasure and dominion.
The irony of cannibalism
Two ironies here: One is that there is an ironic quality to the issue of cannibalism, because it is so fundamentally offensive to a regular old European person that it's almost dramatic irony. "Oh, yeah," the reader might say, "I forgot sometimes people eat each other." That's sublime and ironic, but there is another less obvious irony—the irony of self-consuming life. Cannibalism points to the absurdity of the animal nature. Why should death by cannibal be any more or less emotional than just regular old death? Cannibalism is a fascinating symbol.
The irony of slavery
This novel depicts slavery in an ironic light. Because of the luxury, they create an environment where Tommo doesn't want to leave. Mentally, he strains for comfort, ignoring the chance that they're fattening him up for slaughter, but still, in his body, the physical delight of his slavery is so overwhelmingly good that he cannot help but stay. In a way, his real prison is his inability to resist temptation. He always gives into his desires, even when it's dangerous to do so.
The irony of the ending
It's quaint to pretend that the novel was written and published by Tommo, but of course it was published by Melville, which means the post-scripted epilogue is purely fictional, though it lends itself quite nicely to the story because it gives it the dimension of truth. It is an ironic device designed to clue the reader into the fact that the principles from the story have applicable wisdom for life, because Tommo and Toby reach the same conclusions, in different ways. Their separate points of view remove the illusion of uniqueness—certainly this story happens to everyone, in a way.