Lucky boat or bad betting?

So me and about 5 friends are playing are NL cash game up at school. We usually buyin for around 5$ since we play 2 sessions daily usually.

So I get dealt A9s (clubs) on the button. 1 limper, an all in (which was on .20 more) so I call, SB calls and everyone folds.

Flop comes Qc6c8d. SB bets .25 and I call. Turn comes Jc. Sb bets $1 i reraise 1.50 and he calls.

River comes 6. he bets .50 I raise $1 and then i see him literally shaking as he says he'll put me all in. Now I know from Caro's book he had a huge hand, I figured the boat, but I had to call with the nut flush.

Now was this just a lucky catch or should I have reraised harder on the turn? And who would have folded the flush on the river?

He's shaking, it v low limit and he's not played much, drop those cards.