The Scenic Skyline
1. Top of the Rock: I maintain that 30 Rockefeller Plaza allows for the most breathtaking view of the city - and from here you can see the same view from inside or out, depending on the weather and your own mood.
2. Brooklyn Bridge: an awesome view that should be reserved for pleasant weather; from here you can not only see the skyline but up and down the East River.
3. The Hotel on Rivington (THOR): extremely expensive and since your room consists mostly of glass, it's likely your stay will be visible to much of the neighborhood, but the view from here is entirely worth it.
4. Hotel Gansevoort: dress up in your swankiest outfit in order to peruse the roof deck featuring not only a spectacular view of the city and the Hudson River, but a pool and a bar.
5. Brooklyn Heights Promenade: stroll around the promenade and take not only the skyline but a rare moment in New York where you aren't being pressured to purchase anything. The promenade sits on the East River in front of some gorgeous Brooklyn properties.
6. Empire State Building: Reluctantly added (suggested by JVS) because of the long and intense line you must wait in before reaching the summit. The straight-down view is spectacular, though - but beware the outdoor observation deck during the winter months. It's a bit chilly/windy up there, and a bit crowded. Indoor observation deck located on the 86th floor.
7. High Line: (Sufficiently praised by Uraniumfish) 1.45 miles of park built on a section of the abandoned elevated freight railroad of the West Side Line and winding through the Manhattan neighborhoods of Chelsea and the Meatpacking District. Several entrances throughout.