Buy the Flagship IMO. I just picked mine up today - so haven't built it yet - but it looks a lot more detailed than my QAR (which I do like), and is only going to get harder to come by short of importing. The set is 1.5 years old now, approx, so I don't know how much longer it will stick around?
In comparison, QAR is newer, but also remember that the Myer "sale" price is actually dearer than Big W's every day shelf price for QAR. Big W sell it for $147 every day. Factor in the 10% bonus if you are a Myer One member and they come out a little cheaper, but my point is you can pick up a QAR for $147 any time you like.
In terms of which is the better ship, IF looks far more detailed, for example with my QAR I was disappointed that it doesn't have an upper and lower deck - the hull is "hollow" in that the sides of the ship are like walls while the deck is right down the bottom. It isn't a problem really, but an upper deck would have been nice. IF delivers this - but on the flipside, I really like the minifigs and the decorations on the QAR (the bones, the lantern at the back etc.)