I've stayed at www.azurewaters.com.au in Palm Cove which was lovely, we re-visited there a few weeks back and it was still just as nice. :)

Re: Barrier Reef - Where to stay/visit?
 

I have just got back from the reef. First visit was from a boat off the Whitsundays. It was a sailing square rigger and the trip was amazing. Because of the boat we were in small crowds and the reefs were fantastic. The highlight was seeing a bull ray followed a minute later with a green turtles swimming a metre from me. The skipper would call the local dive boats in advance and I would go down with them. Cannot recommend sailing in the Sundays enough. The place was amazing.

After that we visited from cairns. Cairns felt like a tourist process line and after the uncrowded boat in the whitsundays the place felt crowded. We went on Divers Den Reef quest for $80 on a 80 person boat. For another $80 I got 3 certified dives. No namby pamby glass bottomed boats or semi subs. Quiksilver looked like hell but for non snorkellers probably the best option.

After that we went up to Cape Tribulation. An amazing place in the rain forest with plenty to do. I did another reef trip from there on the rum runner (44 people) and the coral there was in much better shape than cairns. Apparently the rainforest and mangroves clean the rain fall.

My point is avoid Cairns and maybe go from smaller boat. Maybe a vomit comet in rough weather but the reef experience will be more enjoyable.