I've just got back from 6 days in NYC, followed by 5 days in upstate NY - the advice in the others threads is great, but I will say this..
Don't both visiting the Stat.of Lib - just take the Circle line 2hr dusk ferry tour from Pier 83.
The Guggenheim is not partially closed as it's website said before we left.. it's 9/10ths closed...do.not.go.
Times Square is not something to 'visit' - it's something to notice as you're going thru it to somewhere else.
Google for 'Simply Pasta' just off Time Square. Cheap, quick, and utterly stunning food.
We'd read great things about 'The Shake Shack' down by the Flatiron building, but to be honest, we got two burgers, one was 'ok' - the other was cold.
If you can - get on Ebay and get tickets to a Yankees Match before they flatten the stadium. Go and see Avenue Q if you can - the funniest musical I have ever seen.
AMNH and Met museum of Art are both a FULL day each
MOMA is 2/3rds full of the sort of modern art that just deserves total ridicule - but the feature exhibition when we were there was great.
Doing the Empire State Building at Night was a very cunning idea.
Doug