What you need to do if you want to live in San Francisco and work in Silicon Valley: get a (stupidly expensive!) apartment near Caltrain, take an express train down (30-45 minutes, and work on the train), then get the rest of the way to work quickly (helps if your startup is near the train - mine is ~20 minutes' ride, not the greatest).

It's probably not as good as you're getting in New York, but it's significantly better than 90 minutes.