Irony occurs when there is some discrepancy between what we expect and what the reality is. We do not really expect Gulliver to end up in locations where human beings are so very different, physically, than the way we are or he is. First, he arrives in Lilliput, where the humans are only about six inches tall. Then he gets stranded on Brobdingnag, where he is dwarfed by the natives' giant size. Ultimately, he travels to Houyhnhmland, where horses are civilized and run the society, and humanlike creatures are called Yahoos. They are totally uncivilized and used like livestock by the Houyhnhnms. We would certainly be unlikely to expect to see a society where the horses are in charge and use people like we use horses.
Further, Swift employs irony in Gulliver's third voyage to Lagado. There, he sees scholars and intellectuals working on such experiments as trying to extract sunshine from a cucumber or reanimate a dead dog by placing a bellows in his anus and pumping him full of air. We would hardly expect to see such absolutely ridiculous experiments being conducted by people who are like the most highly educated, the most intelligent among us.
In the end, Gulliver decides that the Houyhnhnms really are the master race, agreeing with them about the dirtiness and stupidity of humans. When he returns home, he cannot stand the smell of his wife and children, and he generally finds everyone he once thought so wonderful absolutely disgusting. After Gulliver has spent so long defending his home country, customs, and government to so many individuals, against so much criticism, we would not expect him to turn on his countrymen and women the way he does. This, too, is ironic.