All the known great monsters of Greek myth have been slain. I don't see a problem with a few unique monsters of old still undefeated.
For inspiration you could take a look at the myths of other countries/continents. South America, Africa and Asia would be the places to look, IMO. Eg., Brazilian folklore has legends about a GIGANTIC fire snake who lives in rivers, and punish those who set pasture and forests on fire (look for Boitata). Who is to say that this beast isn't a child of Echidna? Or maybe Poseidon and some mortal woman?
Maybe it lives in a remote place, and because of that it wasn't slain by the heroes of old. Maybe a secluded regio. Maybe it just got lucky.
Then, when the magi find rumors and end up confronting the Greek Boitata, they discover that it's stronger than what they would expect, and largely immune to their magic. It is a unique being born from old myth. Defeating this thing requires researching old lore, understanding how it relates to his mother/father, which are it's weaknesses and creating a dedicated weapon (or spell!) for the task.
(Of course, after killing it the grogs start to spread tales about it, and then you will have several faeries in that role... But none as strong as the original.)