Corrected quote

They are comparable, they are both main villains with very special powers.
I'd say none would win, since neither of them posses what's necessary to destroy the other one: Ganondorf hasn't got rid of the Horcruxes, and Voldemort does not possess the Master Sword nor the Silver/Light Arrows.

But if you'd exclude that, Lord Voldemort. He'd use Avada Kedevra before Ganondorf would get a chance to attack, or use the Imperius Curse to do his bidding.