We will have one chance to visit the Great Barrier Reef during our trip along the east coat of Australia. We will start in Cairns in September and spend 2 months travelling towards Sydney. Should we be taking a trip to the reef from Cairns or Mission Beach or another location?
I'd definitely do it from as far north as possible. The water is warmer so the reef is more colorful. Also, you'll 'run out' of reef about half way down that stretch!
I think Mission Beach would be the best. Cairns seems like it would be really busy and the reef may be a bit more damaged then of the coast of Mission Beach. But you have to get good weather. It has been shocking lately, but maybe in sept it will clear up for a while.
I have to say I only went as far north as Airlie Beach and the Whitsunday Islands, but it was still the best day out of my life: my first scuba dive, snorkelling, warm water (October).
So don't worry - do it when an where the weather and time is right for you, and choose a good company. We used FantaSea. We're normally suspicious of the big companies, but they provided an excellent day out.