I would highly recommend considering an overnight on the reef. I went with a company that had one ship for the daytrip, then for passengers staying overnight, around 5 pm we pulled up next to another ship of theirs (still out at the reef), and overnighters transferred to the other ship.

There was just something incredibly cool about having dinner, sitting on the deck enjoying a drink, in complete darkness, knowing that you were floating above the reef. Then, waking up the following morning and seeing the sunrise over the water was incredible. I can't remember the exact name of the tour company I did this with, but I think there are several. If you're interested, let me know and I can try to dig up the information.