Having grown up and now living in the NYC area, and having spent 2 recent years of my life living in Chicago, I am declaring myself an SME on the subject!!!
My unbiased opinion- NYC thin crust style by the thinnest of margins (think Bush/Gore in 2000). They both have positives: thin crust is easy to eat, is nice and crispy, stays hot longer, and is fantastic cold the next morning when you're hungover. Chicago style is hearty like a meal, it has limitless toppings, more cheese than you can imagine, and it fills you up on a cold day. That said, the major negative to deep dish is that you feel like absolute crap after eating it. No offense to anybody, but the amount of gas produced by one slice of Giordano's pizza could send an SUV cross-country!!!! The other negative of deep dish is that very few places do it right. In Chicago I sampled 10-15 different places, and only 3 or 4 were worthwhile. Thin crust in NYC is done well by so many places, you're never anyplace without good pizza.
Top places:
NYC- Lombardi's (I agree), Grimaldi's (must visit), & John's (6th and Bleecker) are the famous places. 2 additional favorites are Rosa's (3rd btwn 34th & 35th) and NY's Famous (2nd and 41st).
Chicago- Gino's, Giordano's, & Amato's.