We did the Whitsundays before children so 6 of us took a boat out for a week, which was fabulous. I am not sure if I would be brave enough to do over night on a boat with kids. Hamilton island was the biggest, Whitehaven beach and lookout are both a must. We had a lovely night of entertainment on South Molle island which looked smaller and quieter. We did lots of snorkelling and Manta Ray Bay was great. We flew to Perth this year with a 2 and 4 year old and the flights were not bad at all. We flew Emirates and they were great. We had lots of bits to entertain the kids but the in flight entertainment was excellent too.
Sydney - the Aquarium which is in (I think) Darling Harbour; there's also a zoo there. Then a boat trip over the harbour to Taronga Zoo, which is really lovely.
A boat trip round the harbour
A trip up the 360 Tower. You should be able to go early evening with the children (but check that first). If you can't, get your sister to babysit so that you and your partner can at least have a drink there! One drink should just be about the time it takes for you to revolve once - fabulous views over the city.
We stayed on Hamilton island in the Whitsundays, which was beautiful. It was recommended by the travel agent at Trailfinders who helped us plan our itinerary.
We are planning a trip to Oz next year (Jul/Aug) and would be grateful for any tips or recommendations (kids will be 3 + 5). Plan is: 8 days in Sydney staying with my sister 5 days in Whitsunday Islands (which one?) 10 days around Cairns (motorhome or car?) Thanks!