[Wingco]

just returned from there myself early Oct - and unseasonably warm it was there too - 29 & 30 deg C!!
my 3rd time there in 13 months, 7th visit now - love the place, just chilling-out and soaking-up the madness that is NYC.

Someone has already mentioned it, but I hadn't heard of the Highline until my last visit. Pleased I sought it out - fantastic what they've done.
You can do Brooklyn Bridge, Staten Island Ferry and financial district/wall st, battery park etc same day - you did need to pre-book to visit Ground Zero memorial back in Aug 12 & Mar 13 when I was there, but just this Aug seemed no pre-booking NECESSARY, although I HAD pre-booked and we seemed to whizz through much quicker.

Go take a look at Grand Central Terminal - absolutely fabulous.
Empire Hotel (just off the bottom-corner of Central Park, Columbus & 63rd St i think, has a roof-top bar, as does the Peninsula Hotel, corner of 5th Ave & 55th st, although November, will be chilly up there! It was cold in March, but mercifully very bright, dry and no wind. Worth heading up to either roof-top bar just for the experience.

You might not be fussed about Apple products, but the Apple store on 5th ave, just across from the south-east corner of central park is worth going to see - it's the one which is basically a glass cube above ground, with the store - open 24/7, below ground.

USS Intrepid Air/Space museum was great - went in 2002, but again just this Oct and so much more to see/more exhibitions, and of course they've got a Concorde and now the Space Shuttle pavilion.

Can recommend SaraBeths for breakfast or a brunch (Park South - at the bottom of c/park over towards 5th ave), but the queues can be long - especially for brunch on sat & sun - food (and service) worth it though.

Faces & Names bar on 54th st, beside the London NYC hotel was pretty-good, and the Longroom bar - can't remember where (you lose track!!) good too.
Sadly, most of SouthSt Seaport area, inc bars & restaurants, is still closed due to damage caused by hurricane Sandy last year. Heartland Brewery down there not reopening, but their site in the Empire State Building - corner 34th St & 5th ave, IS open and was ok for food, great beer-hall down in the basement - not at all as seedy as it sounds!!

Bowery Bar, Balphazar (think that's how spelt) all good.
If you're up upper west side at all, can recommend Citrus restaurant & bar for evening meal, and not sure if the Odeon bar / restaurant still open - food & atmosphere was good but going-back to '03...

Again, as others have said, get yourself up "The Top of the Rock" - Rockerfeller Centre - MUCH bigger area to walk around and enjoy the views - a less interrupted view north of Central Park, and to the south, you'll get to SEE the Empire State. However, I would also do the Empire State building if you can.

Subway and buses are simple, flat rate fare but if you're there, buy a Metrocard either fixed sum or fixed duration. Think rides are $2.25 a pop now.

I've only ever flown into/from JFK, but all yellow-cabs have a flat/fixed fee from the airports to anywhere in Manhattan - think it was $56 in Oct. Just make sure when you exit the airport building to head to one of the authorised yellow-cab stands - there'll be a guy on duty hollering/blowing a whistle to call the cabs, and probably a queue: very easy to emerge from the airport building looking like a tourist and be picked-off by one of the many taxis/private cars touting for business, nothing wrong with that, but they don't have the same flat fare guarantee. For the return to the airport, get your hotel to book a lincoln town-car company or something, or their own service if they have one - only another $10-$20 on top of regular yellow cab fare (which is NOT the same flat fare as coming in from airport, but then not THAT much more in any case).

I'm not into museums, but Nat History museum IS good - if you go, it's actually free, but there's a well-worded/shown SUGGESTED donation/entry fee. It's up to you what you pay. Good small zoo in Central Park, but not sure if it will be closed for Mid Nov. Never yet got to Guggenheim or MOMA.

Loads of top designer shops on 5th ave. Go into Armani and take a look at the amazing, self-supporting concrete sculpted staircase!
If you're intending to go to Macy's (34th St), go straight to their visitors centre on the mezzanine with your passport and use the self-service touchscreen kiosk to obtain a visitors' discount slip - think it's worth 10 or 15% of all purchases whilst you're there in Macys (i.e. over several days), but sometimes if they've got items on sale the sale discount will be more - and they usually don't offer both.

Enjoy it, and don't worry about trying to fit it all in on your first visit - you'll be going back!!!