The Ender dragon, definetly. You have to climb up ~20 0bsidian towers and destroy the crystals before you can even harm him.
Well, I'll say Wither, as he is harder to his and he is stronger and deadlyer then the ender dragon, as he can give you effect that can hurt you also, he can fly away when you shot a bow, with the ender dragon you can shot the becons they won't move anywhere.
It's harder to get the Ender Dragon. Only THREE strongholds spawn in your world, and you need an ender eye to find it...and you have to bring loads of food, etc etc...