The main point of comparison would be in the way that Chaucer views them. The pardoner and the monk are both members of the clergy, an institution that Chaucer typically holds up for ridicule due to the corruption within it. The level of this ridicule varies from less extreme for the monk to more extreme for the pardoner.
In the prologue, the reader quickly senses a contrast between what monks are supposed to do and what THIS monk does. Generally monks spend their days cloistered in a monastery, observing vows of poverty and chastity, and studying religious texts. This monk, however, enjoys riding his horse, hunting with his dogs, acquiring fine items, and flirting with girls.
He gave not of that text a pulled hen plucked
That says that hunters be not holy men
Nor that a monk, when he is reckless, careless of rules
Is likened to a fish that's waterless,
That is to say, a monk out of his cloister. monastery
But the text held he not worth an oyster.
Clearly, the monk knew he was acting in ways that were against the strictest teachings, but he did not care. He is described as rather likeable for most.
The pardoner is treated with a little more disdain by the author. He holds a much higher, more respected position and uses it to cheat the faithful people out of their money. He supposedly brings pardons from sin and hell to the people which makes them revere and even fear him. He is physically very ugly and effeminate whereas the monk's only physical flaw is baldness and heavy weight. His worst attributes is selling fake holy relics to the people, preying on their hopes for health and prosperity.
For in his mail he had a pillowber Which that he said was Our Lady's veil. He said he had a gobbet of the sail piece
That Saint Peter had when that he went
Upon the sea, till Jesus Christ him hent. He had a cross of latten full of stones brass
And in a glass he had pigs' bones.
The pardoner is using his position to steal money from poor believers; this makes him more repugnant than the wayward monk.
This is a very astute question to ask, because actually, although overtly the Paroner and the Monk dwell in very different social spheres, and the Pardoner is far more overtly disapproved of, both are shown by the somewhat ironic narrator to take advantage of other people to sustain themselves. Let us consider how both are compared and contrasted in "The General Prologue."
The monk we are told is a proud man, who loves sports and has a number of good horses. He also has different, and more tolerant, views than might be expected of the monk:
Being out of date, and also somewhat strict,
This monk I speak of let old precepts slide,
And took the modern practice as his guide.
The narrator wryly notes that the sleeves of his fine garments were edged with "squirrel fur, the finest in the land" and he wore "an elaborate gold pin." All of this extravagant details as to his wealth cause the narrator to concede that:
No question but he was a fine prelate!
Not pale and wan like some tormented spirit.
A fat roast swan was what he loved the best.
His saddle-horse was as brown as any berry.
So, reading between the lines, we can see that the narrator is gently poking fun at the way that the Monk uses his position to indulge in his favourite pastime (hunting) and to keep himself in wealth.
The Pardoner is described as a much more disreputable figure who openly exploits the ignorant to gain wealth. He openly admits how he tricks people, and the narrator comments:
In just one day he'd pick up far more money
Than any parish priest was like to see
In two whole months. With double-talk and tricks
He made the people and the priest his dupes.
He has a rather unsavoury appearance, with the narrator highlighting his "yellow" hair which hung "in meagre clusters" and in "rat's tails." He has "big bulging eyes" and it is suggested that he is a eunuch, because his face is so smooth the narrator mistakes him for a "gelding" (a horse that has been neutered).
Thus, though the Pardoner and the Monk are obviously two very different people in terms of their social position and their appearance, with the Pardoner being far more disreputable than the socially acceptable Monk, both are rather ironically shown to profit from their involvement in religion.