I may be incorrect, but a well-equipped, higher level Incarnation might also do great against these dangerous drakes. Just make sure you have a way to target flying units, and enough speed to keep the initiative.

My advice would be to get an army of Hobbit Slingers. Those things are very tough!

Funny, I never really have trouble with Great Drakes compared to Sky Drakes. Great Drakes are simply too slow to pose a problem to my heroes. If you fight Great Drakes with units with 3 or greater movement, the Great Drakes should never get a chance to attack you. Sky Drakes have 4 movement, so they can close to attack super fast and nothing with less than 5 movement (and that's the bare minimum, and usually not enough if there's a big group of them) can escape.

Sky Drakes also have the nasty habit of teaming up with Djinni and occasionally Storm Giants, both of which are much nastier than the Hellhounds, Efreets, and Fire Giants the Great Drakes tend to team up with. Still, a properly equipped Malleus the Magician can solo a Sky Drake nest if his player is careful, and Great Drakes are a snap. If you can make him invisible and flying, he can wipe them all out without moving.