i'd strongly recommend something less powerful than a 600 when you're coming from a 200cc bike... Especially for "riding in NYC." a twin (SV650, EX650) would be better suited for city riding.
But if you're asking which of those 2 bikes is better, I have to say the Honda. frankly, you are not a good enough rider to make their track prowess an issue. And that's not an insult - it's just a fact. Only the absolute most skilled racers will be able to show as few tenths of a second difference between an '09 CBR and an '09 ZX6. With that in mind, clearly the Honda is the better choice.
Every review out there applauds the Honda for being easy to ride, easy to live with, and dead-nuts reliable. I own a Honda and a Kawasaki, so I like both brands, but look at the last 4-5 years of 600cc sportbike reviews. the Hondas consistently get a lot of praise. the Kawasaki was dead last in 2008, and now first in 2009. They're making drastic changes, which is good when they work, but it also means their design isn't as proven.
Honda all the way. it'll run for 40k miles or more, hold its value well, and you will NEVER notice that it's .1 seconds slower around the track you're not riding...