Having been to Manhatten once or twice, I'd recommend:
Rotating restaurant at the top of Marriott Marquis Times Square ( as in When Harry Met Sally)
Top of the Empire State Building (a bit common, though)
Battery Park next to the Globe statue looking towards Lady Liberty
At the foot of the Statue of Liberty
Rockerfeller, either in the plaza, or at the top.
Lots of romantic nooks in Central Park
Outside the New York Museum (my favourite as I love Ghostbusters, think stone lions at the beginning of the film)
Grand Central Station, the ceiling is beautiful, covered in stars
After a good Broadway show (Phantom Of The Opera is great, and I hate musicals!)
Best of luck