Personally I'd go with the Qantas bus as long as the incoming flight is to terminal 3 (which being BNE/SYD it would be). Between 6am and midday the buses leave every 10 minutes - if you're worried that it might go out full make sure you sit (or stand) right next to the door to make sure you get on the first bus out.

From a theoretical perspective, if you were arriving in T2 (flights 1600 and above) then it could be a different story as you need to go all the way from T2 to T3 (walking past the train station in the process), and re-clear security to get to the bus. In this case, catching the train is probably a better option.

Plus, the bus is free. The train is about $5.