Rooftop terrace at the Metropolitan Museum NY. It's not as touristy as top of the rock or empire state, but it has a stunning 360 view of uptown NY and Central Park. I personally find it an overall classier experience. It's usually not that busy up there so you'll have some privacy, plus it's free! (except museum admission). You can take your GF for a nice museum visit and then go up to the terrace for a nice glass of wine (they may even serve champagne I think) and then pop the question. She will be caught off guard whereas I think a lot of "romantic" place may feel like a set up.

I had dinner at Cafe des Artists one time (overrated place by the way), it's often touted as one of the most romantic restaurants in the city where many people go to propose. The table next to us was doing exactly that, the girlfriend obviously caught on as soon as they walked in and so did we at the next table and all the staff. The two lovebirds were very nervous to the point that our table decided to leave early to give them some privacy.

I second flatfeet's suggestion. And then, following your proposal, have an elegant picnic in Central Park...or go to a diner and have the best grilled cheese and tomato sandwich you'll ever remember. Nothing is more romantic than that!

Check this out:

http://www.thefrenchmanor.com/

I've never been there, but this is where a friend proposed to his new wife. They love the place. And it's not too far from you.