Jen,
I'm no expert on the location but I can tell you what I thought about my diving there last year.
I went on a liveaboard trip with Pro Dive Cairns and can recommend them wholeheartedly. Great staff, great boat, world class dive sites as you might expect.
IIRC, they run their OW courses on "land" in Cairns for the first 2 days where they do the confined water activities, and then you go out on a 3 day liveaboard where you finish off the course with the open water dives.
Whitsundays in my experience were absolutely breathtaking scenery, great for a sailing trip and sightseeing but diving there was not, for me, as exciting as the outer sites of the barrier reef I dived out of Cairns (granted, I only did one dive in the Whitsundays so did not see a massive amount).
So to answer your question, if I had to choose, I would go to Cairns to dive. Wouldn't be disappointed to go back myself.
Awesome social life there too, very easy to find people to hang out with in Cairns and on the boat as the flow of backpackers is strong.
My 2 cents.
Cheers