I'd have to say in response to the query that you can get great food in any city you visit---you just have to know where to eat and be prepared for the excellence found in indigenous cuisine. It goes beyond just great tasting food on a pretty plate. It's why gumbo and jambalaya taste best in NO and LaFayette, LA. And why bialys are so good in NYC and pulled pork is superlative in Wilson, NC or Memphis.
But to answer you question specifically, I'd have to say that San Francisco and Berkeley, CA are my favorites. Sure, there's wonderful food here in NY, but I tire of the "I'm fabulous, and you're probably not" attitude that comes along with the service, coupled with people pushing that disgusting foie gras on me all the time. (Sorry, fellow CT Craft diners, it's a personal aversion.)
San Francisco and Berkeley have the fortunate advantage of close proximity to the highest quality organic farms and dairies that produce some of the most flavorful food in the country. Also, the service approach is more of the "I'm OK, you're Ok, let's find what we have in common" mentality. The server and the served enjoy the dining experience together. Chez Panisse is my favorite, but Gary Danko's cuisine ( I met him when he was chef at the Ritz) was a great experience too.
By the way, I went to see Ruth Reichl (Editor-in-Chief of Gourmet, NY & LA Times restaurant critic) speak at the 92nd St. Y last week and she was asked the very same question to which she answered NYC after a bit of a pause. I couldn't help feeling that she chose her answer to please the crowd (for the most part, short, cranky old NY women). Judging from earlier passages of her lecture, in another place, she may have chosen SF, too.