Although I do love NY, I really prefer Chicago in the end. Apart from cultural differences, there are several reasons why I prefer Chicago.
1. I think the setting along Lake Michigan is nicer than Manhattan's in NY Harbor. Next to Chicago is an enormous body of water, while Manhattan is mostly surrounded by narrow stretches of water, and then the other boroughs. Granted, I love the view of Lower Manhattan from the Statue of Liberty, but only Lower Manhattan can be seen. From a boat on Lake Michigan, one can see the entire length of Chicago's skyline, from the Indiana border all the way, if its a clear day, to Evanston and Wilmette. Its overwhelming how beautiful it is.
2. Chicago is a better setting for skyscrapers. NY's great scrapers are often hard to pick out among the other buildings. The island is so dense that, while the tops of some buildings can be seen (from the Brooklyn Bridge, for example), thats about all you will see. The scrapers are essentially "drowned" in a sea of not-as-good scrapers. Chicago is not as dense as Manhattan, so buildings can easily be picked out in a skyline view. Furthermore, it is easy to get views of many of the buildings from top to bottom from a distance. For example, its hard to find a view of the Empire State Building equivalant to this one of the John Hancock Tower:
There are also some hard-to-describe differences in the overall feel of the city, so I'm not gonna try to explain them. Also, in terms of quality of life, I like that its possible to own a home in Chicago, or very close to it, for a fairly reasonable price. I like apartments and all, but in the end, eventually I'll probably want a house, and some of those in Evanston look pretty nice...
The one huge thing Manhattan has on Chicago is this: New York is cold in the winter, but Chi-town is DAMN cold. It hurts to be outside on some winter days in Chicago.
So, in conclusion: NY and Chicago are both great, but I like Chicago slightly more. Its not surprising to me that some people like New York more, of course. Its just like Annie Hall vs. Manhattan. Its a matter of taste.
And in the winter, I like any Southern city better than either