Can also thoroughly recommend wavelength! I went with them in 2008 from Port Douglas and it was one of the best days of my life so far.
They use a small boat that carries maybe 20 - 25 people so not only do you get a better, more personal experience but you get to go to better reefs that the larger boats can't reach - means less damaged reefs - better wildlife (giant turtles!) and less people to bump into.
Add to that the fact their staff include actual marine biologists who actually care about the reef and you'll be in for an incredible day out. They put on a great lunch and presentation too.
When I went out there at the start of August, it was hump back whale migrating season and we were lucky enough to be met by a family (Large male and female with a youngster) who all put on a show for us! literally 20m away from the boat they were jumping out of the water and splashing around and they swam directly under the boat a few times too.
Again, being a smaller boat, we were able to get right into the thick of the action without disturbing/scaring them, while a couple of the larger tour operators spotted the action but had to stay well back (200 - 300m) because they just couldn't risk getting any closer.
Here is their
facebook page. They post pictures almost every day of what they see on their trips, if you're looking for inspiration.
I'll leave it there.. I just can't sing their praises enough!