The permanent piece called "Meeting" at MoMA PS1 is an etherial experience of light and color and quiet. Sit and look through the cutout in the ceiling and watch the light change both outside and in. You can't tell what you're looking at until maybe a bird flies by.
The Frank Stella's are the best. They are all over the city and they always look amazing. Two of my favorites are the Saatchi and Saatchi lobby (pictured) and the Citi Corp building in Midtown.