Giant Skeleton, like any other Tank is best countered with swarm.
By far the best swarm in the game is the skeleton army. But I've been countered with, and have been countering with a Witch or Barbarians, the later being quite popular among my enemies.
Pretty much anything that will keep him busy long enough to die, before reaching your towers.
The best strategy I'm aware of is to wait for it to come on your side of the map, and then place the army around him. Even if the enemy has arrows or something similar, the skeleton would'be dead by the time they react.
Good point worth mentioning is, flying swarm is not good, as the skeleton ignores them and keeps going to the tower. It will die eventually but not before dealing 1000+dmg to the tower ...