The first thing that I would cite as a metaphor in this essay comes in the fourth paragraph. There, he talks about a child that has just been "dropt from its dam." These are words that you would use for an animal being born. So I see this as a use of metaphor -- he is comparing the children to animals.
Later on in the essay, he uses the same sort of metaphor, suggesting that 20,000 be kept for breeding. Again, he is comparing the children to animals.
By having his satirical speaker do this, Swift is adding to his major point -- he is using this metaphor to show how the authorities generally treat the Irish as animals.
There are numerous metaphors in Swift's "A Modest Proposal." In addition to the two mentioned above, Swift uses mataphor when he writes:
I grant this food will be somewhat dear [costly], and therefore very proper for landlords, who, as they have already devoured most of the parents, seem to have the best title to the children.
When Swift uses "devoured" he is using metaphor. He is comparing physically eating to financially destroying. What he is trying to elaborate on is the landlords' financially destroying their tenants (this would be the tenor of the metaphor). He uses devoured (the vehicle of the metaphor) to explain that financial destruction.
The word "title" is a second mataphor in this passage. Title here is used as it would be used to designate owned property or land. The landlords have title to the babies to be devoured, because they have already devoured the parents. The right to eat the children is being compared to property rights.
"dropt from its dam"
"already devoured most of the parents"