Your right, the whole city is a great location. I particularly liked going up the Rockefeller at night, gives you amazing views of the city all lit up inc the Empire State and the world trade in the background. Liberty Island ferries are great and cheap. Get you to the Statue of Liberty and Ellis Island, great shots from the boat looking back at Manhattan. Central Park is also brill for some shots, we went at Xmas so the place was all lit up. I wish I had got more 'street' shots with the subway steam coming up through the drains.
Also the big red bus tours take you down some side streets you may not walk down for some less iconic 'new York' snaps. A must would be taking a stroll across Brooklyn bridge too.
(Possibly not great for taking some shots but I recommend 'The View', it's a rotating restaurant above the Marriott hotel in Times Square. Pre book online).
I also wish I had got some subway shots but we only rode it once.
Book yourself some basketball or ice hockey tickets too, both times I've been I've seen the Knicks, most recently Knicks vs Brooklyn which was electric.
Oh and don't give any money to the dressed up characters in Times Square. I made that mistake because I didn't want to get shot but there's signs saying not to give them money!
Try a long exposure in Grand Central station, that'll look cool with the amount of people buzzing around, just sit your camera on the ledge at the top of the stairs. I tried....failed :-(.
If you get the chance to go either to New Jersey or Brooklyn then no doubt there'll be some great spots to shoot back into Manhattan.
We also loved the 9/11 museum, very emotional but certainly worth the visit.
Again we pre booked this before we went but Aladdin on Broadway is phenomenal!
Just remember, up the Empire State in the day and Rockefeller at night!
I'm not jealous at all that your both going.....(browsing Virgin holidays as we speak...)