Well, I have to admit that I am a bit biased since I am a lifelong New Yorker, and have only been to Tokyo one time for a few days. My impression of Tokyo was lukewarm. It is an amazing city, the only problem I had was that it was not as tourist friendly as I thought it would be. Japan is notorious for not liking foreigners living there, but I thought it would be a little bit more friendly to tourists. There is a pretty decent amount of English language signs and announcements on the subways and in the airport. Contrary to what many westerners think, most Japanese speak little to no English. This is frustrating when it comes to negotiating directions and prices.
Not many Americans speak Japanese either, but who should learn whose language? Both countries are rich self contained economies where the citizens don't have to really learn any other languages to make money. That's the reason why the Japanese don't need to learn English. It's understandable.
Some other differences between NY and Tokyo besides NY being more tourist friendly, and that its subways run 24/7, Tokyo's shut down at night. Tokyo is safer yes, and cleaner. The Japanese are pretty nice people who are pretty helpful when asked for assistance. New Yorkers are notoriously rude, but that attitude is dieing down. NY has diversity Tokyo doesn't. NY could teach the world a lesson on how to live multicultural, it's a microcosm of the world. There isn't even a "Little America" in Tokyo that I know of.
In terms of the cityscape I didn't really see enough of Tokyo to accurately judge. It is laid out more like LA in that it's spread out and a bit decentralized which makes navigation a bit intimidating. NY however, is nicely broken up into manageable pieces that allows the visitor to digest the city a little bit at a time. Tokyo's skyscrapers are clustered in several districts spread throughout the city, NY's are too in a way but are more centralized in various parts of Manhattan. There are a lot of nice areas in Tokyo that have trendy shops and what not, like NY. Tokyoites are among the most stylish in the world, but so are NYers. The Japanese do have an interesting distinct style about them, but again so do NYers.
Japan does have a lot of hot Japanese girls, but so does NY. Both are style capitals. I'd say NY does have a better skyline, and that will be even more true after the World Trade Center is redeveloped.
I was hearing that Hong Kong is better and more tourist friendly than Tokyo is to westerners. I will be in Hong Kong in a few weeks and I can't wait. I really want to compare HK to NY. Both are amazing cities. I can't wait.