Having lived and worked (food related) in both locales, I vote for San Francisco over New York as the better place for a Chowhound to live. Manhattan may be more densely populated with restaurants and have a leg up wider variety of some cuisine, but San Francisco has more of what I love to eat. When I'm in San Francisco the only things I miss about New York are a good slice and the pork buns at Momofuku. When I'm in New York I miss a good burrito from El Balazo on Haight or the carnitas at Tres Hermanos in Napa. I dream of the pork belly, salmon rillette and foie at Bouchon in Yountville (Bouchon in Time Warner just isn't the same). I dream of a double double at In 'n Out (the Shake Shack doesn't hold a candle to it). And if I'm in NY for more than a month I get an unexplainable craving for a Krispy Kreme (even though I rarely think of going there when I'm in the SF area).
Yes, NYC has a plethora of fine dining options for those fancy pants occasions. I've been a fan of Gramercy Tavern for special occasions for years. I've also eaten at Per Se and love the exquisite food and ambiance, both peppered with the kind of subtle intelligent humor that I love. But with options like Cyrus, Chez Panisse and The French Laundry, I'm satisfied with the SF Bay area.
And when it comes to availability of fresh produce San Francisco wins hands down. Nothing comes to mind when I think of produce I long for from the NY area, or any particular vendor at any of the Green Markets that I just can't live without (except for the guy who used to sell raw milk at the Union Square Green Market on Fridays, but last I heard he was only selling at the one up by the Cloisters on Saturdays--haven't made it up that far, even though the milk IS worth it). But SF has an abundance of produce about practically all year. I never knew I liked brussel sprouts until I had some off the stalk. Blood oranges are an addiction I wait to sate every January. And don't get me started on berries or stone fruit! Even fresh butter, cheese, and eggs are abundant and delicious at almost every farmers market I can think of in the area.
Even grocery stores are more Chowhound friendly in the SF area. Yes, NY has more (in number) "ethnic" markets, but the only grocery store I go to in NY is Whole Foods. In the Bay Area I love the Berkeley Bowl and Ranch 99. The SF Chinatown may not be as spread out as the one in NYC, but if you know where to go you can find what you are looking for (that's way it is with 'Hounds).
Seafood is better in SF, too. With the exception of soft shell crab, SF just has better, fresher fish (in my opinion). After all, King Salmon trumps Atlantic Salmon every time.
So what do other Hounds think? I'm not looking to pick a fight, nor am I saying Manhattan isn't a great food town. I'm just saying if I have to choose one of the other for my primary stoming grounds, it's the San Francisco Bay area.