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Hi jenna, The weather in September can be very hot or it can be in the 70's (F). Bring an umbrella b/c we get rain then too. Harlem is being revitalized now. I'm not saying it is all great, but there are some very la-di-da areas there. Former President Clinton has his offices there.
Go to Cenral Park, there is a lovely zoo there. It is huge and does border up into Harlem. That's the bad part. You could go up and down 5th avenue. That's where FAO Schwarz (Toy Store), Trump Tower, Huge Toys R Us, sachs and Rockefeller Center are. Empire State Buliding, ground Zero, .
In Queens you could visit Flushing Meadows Park. That's where the big Hemisphere/Globe thing is. It is in a lot of movies. There is a small zoo, museum and picnic area. The park is the old World's fair grounds.
Back to Manhattan... there are Seinfeld and Sex in the City Tours in addition to the tourist bus tours. I am bad b/c I have lived here all my life and have not gone to see things people travel to see.
Where are you staying?