There are heaps of tours to the reef in Cairns you can pick and choose until the cows come home and still be confused...so I'll break it down, what I wanted out of a reef tour.
!/. Minimum numbers on the cruise..100 tops
2/. An operator who knows the area you are going too well
3/. Good explanation of the natural habitat
4/. Good safety
5/. Nice food
6/. Well inclusive tour
Seastar has this, they are not one of cheapest cruise out there, but they are one of the best.
On the cruise we had a marine biologist, who came out with the snorkelers and explained the types of reefs we were going to. She explained the types of fish that would be at the reef and how to approach them without touching them.
On the way home, the crew undertook a mock "Man Overboard Rescue", which was needed for their accredition, but involved all the guests. The things you learn at sea, it isn't easy trying to find people in the water, especially with high waves.
Their safety briefings to the guests were first class, easy explained to understand.
They go to the reef areas on the out limits, but arrive there before the crowds and move onto the next area before the crowds catch on.
A great dog out...we'll be back again.