IMO bay area fine dining cuisine is #1 in the nation right now (NY might have even be #3, had Chicago not have some unfortunate chef deaths in the last few years)
If you look at new york times's 4 star restaurants list:
Le Bernardin/Jean Georges (old french cuisine, tons of sauces, boring)
Per Se << French Laundry
Del Posto (mario battali's strong/strange flavors are either love/hate) Quince (sf) is much more consistent and tasty.
Sushi nakazawa - very good nigiri, but lacks decent cooked seafood. Yoshizumi (sf) is much better in both nigiri/cooked food, taste great, is cheaper, and the place has a great minimalistic japanese feel.
And there's no direct answer from NY to Benu (out of this world Chinese), atellier crenn (if she only did desserts for all courses), saison (highly innovative), californios, mourad
SF might be in top five cities in the world right now for great food (low end and high end)