Graffeo roasts the best coffee. Dark roast, light roast, and a blend of the two; also comes in decaf. My preference is for the dark roast. I have been drinking it for 41 years, and it is consistently roasted just dark enough and without a lot of bitterness. I believe it makes the best cup of coffee anywhere. But you don't get a cup of coffee in their shop, only beans. You can order on-line, but you must drop by the shop on Columbus if you are in San Francisco. Little Italy is it's natural home, and you might get a story or two from Luciano if you are lucky.
White Crane Tea not only sells Japan's highest quality award winning tea, but an amazing array of professionally hand drawn scrolls and highly sought after Japanse Hagi Pottery (Hagi ware, Hagiyaki). The friendly proprieter David Furukawa-Chen is extremely knowledgeable about formal Japanese Tea Ceremonies and won't hesistate to answer all your questions about tea and art. Don't forget to check out the reviews on yelp; http://www.yelp.com/biz/white-crane-tea-company-san-francisco
Drinking a central coffee right now, and the blueberry bran muffin sitting next to me is spectacular! This is the epitome of a quiet neighborhood coffee shop, with babies and dogs and regulars saying good morning to each other and the baristas are often on a first-name basis with customers. Good food, good coffee, good vibes.