You can get wonderful views of the harbour and Circular Quay from the South East Pylon of the Harbour Bridge, which is open to the public between 10:00 am and 5:00 pm. The entry fees are fairly cheap and there are normally no restrictions on how long you stay up there. Photography is also not restricted.
I had to tweak this image in Adobe Lightroom to darken the sky and lighten the foreground.