Haven't dived the Far Northern Region of the Great Barrier Reef (GBR) for many years but the Cod Hole / Ribbon Reefs and Osprey Reef are fantastic.
Here is a website that might help you - www.divingcairns.com.au - it has info about day trips out of Cairns, 2&3 nighters and longer.
Cairns is basically a largish (by Australian standards) city and is used as a base for trips to the GBR as it is closer to the Reef than Townsville, The Whitsundays, Mackay, Gladstone or Bundaberg which are the other major centres along the lenght of the Reef.
Cairns and The Whitsundays are also the major tourist centres as well so there are lots of boats and therefore day trippers etc so if you don't like crowds then look at another region.
Also beaware that it is still in our cyclone season (like a hurricain but bigger) in northern Australia so there is always a chance that one might blow up whilst you are out there or before you go - in which case the trips can / will be cancelled. The up side is that there is ussually less tourists 
Hope this helps.
Karl