I have lived my whole life in the NJ/NY area, so I am conditioned to most appreciate thin-crust pizza.
That said, New Haven has the best pizza. Take your pick, Sally's or Frank Pepe. I've had what I consider to be equally good pizza at the Frank Pepe in West Hartford, although some claim it's not the same if it doesn't come out of the original oven on Wooster St.
What Chicago has... it may be good, but I'm reluctant to call it "pizza". It's really a different food. Yes I've been there and had it. Not my cup of tea, but I don't begrudge Chicagoans their love of their home-town food. Likewise, if Cincinnatians (?) can actually enjoy Skyline Chili that's their business.
Sometime back in the bronze age, I was in California for grad school for a year... couldn't find any good pizza. One day, I asked someone if there was anywhere I could get good pizza. They said "Domino's". I said "No, *good* pizza". They said "What's wrong with Domino's?" Thus ended my search for pizza in CA (I imagine the situation is somewhat better nowadays). Also couldn't find a decent bagel to save my life, but that's another story...