Having written a 15 page research paper on the North American Video Game Market Crash of 1983 and how Nintendo revived the market, I can confidently say Miyamoto even back when Yokoi was alive. It was Miyamoto's games that made them really successful in the arcade business. Aside from making Nintendo very successful in Japan, this, in turn, allowed them to introduce the NES (initially, in Japan, and then America). It was Miyamoto's games on the NES that made the system, and it was the NES that made Nintendo THE name in video games.
On top of that, it has been his games that have created the bulk of first party sales even through today. He even plays a role in hardware development now. Plus, his philosophy on game development and his ability to mentor newer game designers are invaluable.