To fully appreciate the layers of irony in "The Pardoner's Tale," consider the Prologue to the tale as well as the tale itself. In the Prologue and in the first 200 lines of the story, the Pardoner preaches against vices while at the same time admitting and revealing that he has those very vices.
First he makes it clear that he preaches against the love of money as being the root of all evil, but he preaches only for gain, not out of concern for people's souls. This is ironic on three levels: first, that he would openly reveal his own sinful motives; second, that he preaches most against the vice he practices most; and third, that he is able to actually make men repent of greed despite his own blatant hypocrisy. Here's how he puts it:
Thus can I preach against that same vice
Which I use, and that is avarice.
But though myself be guilty of that sin,
Yet can I maken [sic] other folk to twin
Another irony is that although the Pardoner is full of vice, he is able to tell a highly moral tale, which he proceeds to do: "For though myself be a full vicious man,/ A moral tale yet I you telle [sic] can."
Besides greed, other vices that the Pardoner preaches against even as he practices them himself are drinking, gluttony, swearing, laziness, and revenge. He waxes eloquent about gluttony and the horrors of strong drink, but he would not begin his tale until he had eaten and had some "corny ale."
He concludes his lecture against swearing by saying, "Now, for the love of Christ that for us died,/ Leaveth your oathes [sic] bothe [sic] great and small." Ironically, "for the love of Christ" is often an oath, but in a preaching context, it could be a valid statement, so a listener who wanted to accuse the Pardoner of swearing here could himself be accused of not appreciating a true appeal to the Savior's love.
The story the Pardoner tells decries the laziness of the rioters who want to gain money without working for it, yet the Pardoner admits, "I will not do no labor with my hands." As the rioters seek to take revenge against Death for killing people wantonly, so the Pardoner seeks revenge against anyone who has offended him or his fellow pardoners (l. 416). The rioters act as if they are on a noble mission, when in fact they are merely drunk and trying to show off. In the same way, the Pardoner disguises his revenge with fine phrases: "Thus spit I out my venom under hue/ Of holiness."
Other examples of irony surface when we consider how the Pardoner tells his tale. First, although he says he is beginning his tale at line 462, he actually only barely starts the story before lapsing into a 200-line sermon. He says he will tell a tale to the company's "liking," yet he takes his good time getting to the story. And after he finishes, even though he was supposed to be telling a story for entertainment, he launches into a full-scale sales pitch for his pardons and relics, telling the Host to open his wallet. It's ironic that he has the gall to do so after he has disgusted them all with his honest confessions about the kind of person he is--and when he knows that his job was to entertain.