The hop-on-hop-off bus tour enables you to see the architecture better than on foot, you can hop off to for a closeup of anything that strikes your fancy. The Gray Line "All Loops" tour includes a downtown loop, uptown and a nighttime tour (not hop-on-hop-off); the $49 pass is good for 2 days. So you can spend two days touring around the highlights of the city. Since the bus route time is actually just 2 or 3 hours per loop. you're really spending most of your time on the ground, experiencing NYC firsthand, which I agree is esssential.

By all means take the Grayline Double Decker bus tour. Its a great way to get an excellent overview of The City. The guides are usually very informative.

The following website has plenty of information to help you plan your trip.

http://www.nycvisit.com/home/index.cfm

I'd recommend taking the free Staten Island Ferry. Great city views.
Question for GoTravel (and others): Is the Rainbow Room open again?

Rainbow Room and the separate Grill are open. Take a wheelbarrow to haul your money in.