I religiously watched and read Bourdain, his loss is still a sore sport for me. Him and Jessica Walter.
For North American cities outside of NYC, Bourdain held Chicago, LA, Charleston SC, and Cape Cod (specifically Provincetown) in highest regard. He goes into great detail about each in his posthumous book
World Travel: An Irreverent Guide. I remember he also loved Detroit, Montreal, and Mexico City.
His favorite city in the world to eat though, even more than NYC? Tokyo
(to hauntedhead's earlier point though, I guess he didn't bother trying the Mexican
)