I'd put them tied, myself. Gates realized the computer revolution, and was responsible for putting a computer in every home. Jobs did the same thing with the smartphone and tablet. While you could argue that the latter wouldn't have happened without the former, I ultimately see them both as being equally as important.
Though I do think we'll remember Jobs a little more fondly. Mostly because, and excuse me for being crass for a second, he had the "good fortune" of dying at the height of his career. Sucks for him personally, but it'll do wonders for his legacy. He didn't have to suffer through a period of decline that ends up tarnishing his image a bit, like Gates did with the antitrust hearings, and MS' stagnation in the 00's.
What Apple is going through now would've happened with Cook or Jobs at the helm. The bigger the splash your company makes, the higher the expectations for that company to continue making big splashes. Thing is, no single company can continue producing huge industry changing events time after time like MS did in the 90's, and Apple did in 2007-2011. Eventually, they'll end up disappointing everyone when they go from being truly innovative, to simply iterating on their previous innovations. It's an inevitability. But to Job's advantage, he avoided that downswing altogether, and we'll always remember him as The Innovator because of it.