Ah, good catch about per se. and I haven't had eleven madison park in 3 years; wanted to withhold my opinion. I really wanna go back, but if I'm going for a farm-to-table restaurant, I might as well as go to a restaurant on a farm :)
It's interesting that the NY times critics wield so much power with the chefs and NY public (and maybe even american public), when there are plenty of review systems (michelin, pellegrino) that are more worldly and forward looking. IMO, New York high end cuisine has always been more about hedge fund people and old money impressing each other with higher spend, rather than better food. Maybe that's why there's an aggressive restaurant review culture that serves well to these aggressive customers (born out of finance).
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)