You don’t mention how you plan to travel from Brisbane to the north – Cairns is approx. 1700Km (1020 miles/ 24 hrs non stop) on a not very good two way road – it’s a long long drive and pretty boring most of the way.
As you have limited time I’d suggest flying from Brisbane to Cairns.
Re Fraser Island – to fully appreciate the island you need a four wheel drive vehicle to get around. A couple of options to consider:
Option 1: The fastest way there is to drive from Brisbane to Hervey Bay (300Kms/4hrs), leave the car on the mainland and catch a ferry across to the island and stay at one of the resorts – Kingfisher Bay is quite nice, and then do day trips around the island organised by the resort. The whale watching season ends at the end of October http://www.kingfisherbay.com/ Then return to Brisbane and fly north
Option 2: Drive to Noosa (140Km about 2 hrs) base yourself there and do either a one or two day trip to Fraser Island. Then return to Brisbane and fly north
There’s plenty of accommodation in Noosa at varying price ranges.
The day trips from Noosa take you to the Pacific Ocean side of Fraser so you won’t get to see any whales – they stay on the mainland side of the island. http://www.fraserislanddiscovery.com.au/fraser-island-one-day-tours.html
If you decide to drive to either Noosa or Hervey Bay take the time to drive along the coast from just north of Brisbane. Go north from Brisbane on Highway 1 take the exit to Mooloolaba (Route 70 Sunshine Motorway), exit route 70 and follow the road into Mooloolaba then stay as close to the coast as possible from here to Noosa, route 70 runs parallel to the coast but inland and you miss some great beaches along the way
PS: School holidays in Queensland start on Saturday 20th September for two weeks – so accommodation could be an issue at more popular locations.
PPS: It has been a few years since I’ve been north so will leave that to others to advise. Trip Advisor has plenty of information on North Qld and Fraser Island.
Heron Island is a great dive site too but it’s not far NQ - http://www.heronisland.com/?gclid=CIP2r77M3cACFdgnvQod1KAAcQ