[tallstack]

I would raise the river and call the 3-bet. His check-raise on the flop sounds a lot like 2-pair. I don't see how pocket queens would not raise preflop. Pocket nines are the only other hand that you are behind. I also don't see the 6 on the turn as changing anything - you should be ahead here as well. If the river ace helped him it is only because he badly misplayed a flush draw, or he limped PF with aces. If he has trips then you might not be facing a 3 bet. If he has 2-pair then he likely will call your raise. If he made his flush then you have to pay to see it. Overall, I think that 2-pair makes the most sense and he will pay you off enough to justify the raise.

Dave