What about Darling Harbour. Not the beach, but you have water views? There's the novatel, medina grand, star city hotel.
Maybe the rocks? Don't know many hotels there, and again it's not the beach though....but it's close to public transport and easy enough to get to a beach, or anywhere, if you really want to.
Some good web sites to look at are www dot expedia dot com and www dot stayz dot com dot au they have heaps of hotels and the price the rooms start from. Also www dot lastminute dot com can be good sometimes too!
North side of sydney could be good too, esay to get to both the beach and the city. There are lots of little beaches around there too, around Mosman, Cremorne Point. Again I don't know any hotels there though.
Queenscliff, Dee Why or Curl Curl are north of Manly a little, but I don't know if that's a bit too far?
On the other side would be Rose Bay, Potts Point, Bondi (swiss grand, meriton, ), Tamarama, Bronte, Coogee (medina, coogee bay hotel, coogee sands).

Don't know if any of that helps, but that's all DH and I could think of!! There are HEAPS of beautiful places to go to.

If you think of more questions don't hesitate to ask