From memory (I dived Queensland 13 years ago) the Yongala is an incredible dive, one of the best I've ever done anywhere. The rest of the Barrier Reef was decent, but not mind-blowing stuff. I didn't get to the reefs way off shore/up north, which I hear are better, but it's a long way and therefore expensive.
I dived Ningaloo 3 years ago and that was awesome - among the best diving I've ever done (outside Indonesia, which is hands down the best). The reef is feet rather than miles from the shore and it's not at all crowded, unlike some spots on the GBR. March is the start of whale shark season and there are mantas there at that time too. On a purely diving basis I recommend WA over Queensland any time.
All that said, Perth is a long way from the east coast (of Australia) and Learmonth (the airport for Ningaloo) is another couple of hours flight from Perth.
It's probably worth stating explicitly that Australia is becoming one of the most expensive countries in the world, particularly if you're coming from the US. Food and drink is generally excellent, but it's exceedingly pricey. 10 USD for a bottled beer is not uncommon, 20-30 USD or more for a main course in a fairly standard restaurant is normal. Diving is similarly not cheap - 3 nights on the Mike Ball liveaboard from Cairns is over 1500 USD in the "budget" cabins. Many Americans are surprised by this - Australia is a fabulous place to visit (written with gritted teeth by an Englishman, particularly after Brisbane last weekend...) but you need to be comfortable with the prices before you go.