If you find yourself in San Francisco with any level of frequency, I would first try the homemade Natto at Minako at 17th and Mission. Barring that, find a local natto-liker and ask them where they think is best in your area. Quality varies widely and if the first bit you taste is awful-metallic-ugh then you are not gonna want to try more even if it is better.

Besides, you like Marmite, you'll probably be fine. ;)