We've been to NY several times just for a couple of days at a time. Do yourself a favor. Don't waste time standing in lines for discount tickets. You can get tickets (usually in the last 2 rows) for a lot of shows using TicketMaster pretty cheap. And you can get them in advance so you can schedule them.
I hope you like walking. It isn't necessary, but it is great city to walk. You're staying downtown, so it is a little way to mid-town, but that is where you will see the best sights - the Empire State Building, Times Square, Broadway, Rockefeller Center, the Museum of Modern Art, etc.
But to answer your question, get a CityPass. That will get you into some of the museums, the Empire State Building, a Circle Line Harbor cruise, and some other things. I think it costs about $50 but the face value of the sights is over $100. So if you don't go to them all you will still get your money's worth. Or if you go to a couple (like the museums) and don't find them interesting, you can leave after a short time and not feel like you paid full price for something and didn't use it.
If you see something you like, you can go back. One place I would really recommend is Rockefeller Center. There are several tours that appeal to different tastes - history, television, etc. And if you have a nice day, go to Central Park. Maybe have lunch at the Tavern on the Green (that's in Central Partk).
That's my input. Have fun and enjoy NY. It's a great city.