It is ironic that Ames's brother Edward is sent by the congregation to college in Germany, and, instead of coming home a "great preacher," returns an atheist.
It is ironic that Ames spends much of his time worrying that Jack has designs on his (i.e. Ames's) wife and child, when Jack already has his own wife and child with whom he is concerned.
There is charming irony in the fact that a Congregationalist minister should be so reverential and indebted to the writings of a great atheist thinker.
It is ironic that Jack is named after John Ames, when he happens to be the person with whom Ames has the most trouble in his life.