Some may have Roy.
I recall seeing one ladys video of Sydney Harbour right around the opera house and bridge, she did heave special permission.
All the others ?
I doubt very much permissions could be gained, maybe for GOVCO type promotions / media at certain times.
As you have probably seen CIFT or OpenSky apps, most of the harbour is off limits, most of Botany Bay due to airport locality, but then also councils and of course SHFA ban flights, due to amount of ferry / heli use through there.
City of Sydney may have some areas under their control, they have info here
Filming and photography permits - City of Sydney
More likely the busy part of the harbour is more likely SHFA . . . I think it'd be a nightmare trying to get to the right place here to ask . . .
http://www.shfa.nsw.gov.au/sydney-Resource_centre-Permits_and_applications.htm
Nothing specific I could find.