Try Virgin Blue for your Sydney-Cairns flight.
There are tourist offices in Cairns and Port Douglas where you can book a reef trip. I went out to the reef with a company called Haba. Some companies took as many as 400 people out at a time, where as Haba only took 50 (although I still would have preferred fewer). We mostly dove, but when I did snorkel, even with that size group it was tough to get away from people in the water. I can't imagine being surrounded by 399 other snorkelers.
[This message has been edited by letiole (edited 08-09-2003).]