The irony of slavery
When the young farmer realizes the true horror of American slavery, that is ironic to him, because he has believed the rhetoric in his community about freedom and equality. It is strange and horrifying to him to consider that perhaps those terms were only applicable to white men, but when he sees a slave left in a cage to starve to death, with no one helping him, he realizes that slavery goes against every American principle.
Homogeny and religious freedom
When James sees the Quakers, he sees that although American religious freedom is certainly an inextricable part of what the colonies provide to the settlers who came there, there is an ironic homogeny in their community. The homogeny is even more ironic when one considers the strangeness and mysticism of the Quaker point of view. They are free, but they are strict.
The Russian botanist's irony
The ironic arrival of a Russian botanist shows James a broader point of view about America, because he sees America through the lens of his time in England, but the Russian sees America as a mystical scientific euphoria, because he traveled so far to be there, and because, compared to Russia, America is very different. The contrast that James provides is deepened by the botanist's point of view.
The irony of snakes
There are snakes in America, and Mr. J.B. asks James to describe them. Ironically, they're basically similar to what one might find in England, except different in detail. The irony of the snakes is that it signals the ubiquity of nature. James wanted to believe that America was the dream world he hoped it would be, but Mr. J.B.'s assignment helps him to address the scary aspect of nature, the dangerous and creepy.
The ironic abandonment in war
When the Revolutionary War begins, James realizes that Nantucket is not the right place to be. He departs, one might expect to the Quakers, but instead he goes not to a European colony but to the Native Americans, because he shares an affinity for their point of view of nature. As a farmer, he understands their culture, because it is built around agriculture and the beauty of the land. It is ironic, because most conceptions of natives from this time might have called them savages, but James sees them as people.