The Chef's Table at Brooklyn Fare should be in the top 5 of this list. It is one of the country's most unique and enjoyable dining experiences.
Your ranking is a bit puzzling. Although I am a big pizza fan and have enjoyed Frank Pepe's clam pies, there are certainly much better pizzerias in the country. And, to put a pizzeria above, say, a place like Zahav in Philly, is a mistake.