I think that the operators are all probably pretty good. We went out on Reef Magic from Cairns to a pontoon moored on the reef. That was convenient because you had shade and they had a good buffet lunch on the pontoon. They had a semi-submersible that was interesting. Those people snorkelling will encounter Wally the large Maori Wrasse who will swim up to you for a photo opportunity. We had a good day although it was rough getting out there and back. Luck of the draw, I suppose.
Both boats offer the same experience. They each take you to a different fixed pontoon on the Outer Reef where you can experience the GBR by snorkeling, semi-submersibles, glass-bottom boat rides and an underwater viewing platform.
There are pros and cons for each, but I prefer staying in PD.Edited: 29 December 2016, 23:06
Firstly, when are you going and how many days are you in Cairns ?
Cairns is obviously closer to the airport and easier to move your group around. You can use tours to get to the reef (full day tour) and rainforest/Cape Tribulation.
Port Douglas (one hour drive north) is much smaller than Cairns, has a good beach, marina, restaurants, access to reef, closer to rainforest/Cape Tribulation, has Wildlife Habitat for native animals - for me much nicer place to stay but a lot depends on what you plan to do.
we are staying 2 full days and 3 nights.
If I had just two days I would probably go to Port Douglas. One day on the reef and another walking on the beach and spending some time in town. The pub is great as is the Tin Shed. Plenty of first class restaurants. Classy accommodation but probably more expensive than Cairns.
Cairns is also appealing but has no beach. Still the foreshore walk is great. A lovely lagoon / swimming pool on the foreshore. I love the vibe with stacks of young people from all over the world mixing.
We went with Reef Magic, here is our TA review
Thank you all