PPers know that one of my pet peeves is flat terrain. Neither NYC or Chicago would work for me in that regard. That said, if I had to choose, which I'm grateful I don't have to, I would go for NYC. At least the Adirondacks and the Appalachians aren't too far away. In Chicago, I would have to drive for two days to get to Montana. Illinois is the flattest state in the country.
Even otherwise, NYC would be my pick, because on most counts, it trumps (no pun intended) Chicago. While Chicago has the lake, NYC has the ocean. Chicago's downtown is actually quite a sight, it is more imposing, but NYC's is world-famous, and for good reason. And then there's the weather. While the NYC winters may intimidate someone from warmer climes, it is no match for the Midwestern cold that chills you to the bone. I endured three years in Minnesota, so I can testify to the fact that one grows weary of it very quickly. I'm not sure how important a Pakistani community is to you, but if it is, Chicago, while home to quite a few, doesn't have as many of us as NYC.
Food is a contentious topic. Thin crust vs deep dish is the perennial raging debate. There are people who've actually decided which city to move to based on just this question.