I went diving the GBR in August/Sept '88.. Long time ago but the weather doesn't change I guess, except for a little global warming.
Left Cooktown, went north to Lizard Island, then south along the reef to Cairns 8 days later. The weather was overcast with some rain for several of the days. Otherwise sunny. IIRC there was always some wind. Nothing excessive, 5-10 mph. The thing that was amazing was the isolation. We did not see another boat for days on end. The captain said the best time was Monsoon Season provided you did not have a monsoon. The sea could be a glassy calm and 150 ft Visibility then. Again, IIRC, our vis was in the 75-80 ft range.
Hope you have a great trip. The Aussies are a friendly bunch with great beer.