Happy holidays everyone! I'm a New Yorker in his mid 20's that's visiting Japan for the first time in January! I'm looking forward to ride the JR, which from what I understand that while it can be convoluted, it's tremendously more clean and better compare to the crappy subway that we have here in NYC. I can't wait to see this beautiful country and experience its culture, food, and other fun stuff .
Anyway, I hope that I will be able to contribute to this forum after my short stay in Japan
I adore NYC for many of the same reasons as Tokyo but the trains in either city are none of them!
I will say that once you "get it" the system in Japan made much more intuitive sense to me than the NYC subway system. The inability at certain gates to cross over to go in the opposite direction boggled my mind. To experience the "full force" of Tokyo rush hour I suggest (discourage you) from hanging out around Shinjuku station at around 8:30AM!
If you're saying for a week or more and plan to travel around and not just stay in Tokyo I would suggest you get a JR Rail Pass as it's great for touring and is generally cheaper for continuous longer distance travel. You can get it rush delivered depending on when you plan to be leaving: http://www.jrpass.com/buy_the_japan_rail_pass_online?days=7&passengers=1
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