Bill Gates is smarter as an engineer than Jobs was. He was actually hands on with building Microsoft's products. Steve Jobs was passionate about design and UI. Remember that Wozniak was the one who actually designed the Apple I and Apple II.
I think Microsoft was a more important company than Apple throughout the first generation of personal computing. It was Microsoft who was able to achieve the "A computer in every home" vision. Apple PCs had innovations, but never achieved a market level close to Windows.
Apple, so far, has been more influential in this current age of mobile computing. iPhone and iPad have been much more successful than Windows, and has led the game for quite a while. Even with a higher market share, Android was following Apple in design until recently when they started to push the market design.
So back to the original question, I don't think there is a clear cut definitive answer. I think you could make a good argument for either, and Apple fans would say Jobs, Microsoft users would say Gates. I hedge and say both.