Preflop I would also complete 33 from SB. Folding to tight, and raising will just bloat the pot, when we are out of position with a hand, that does not flop well. If people are bad enough to limp, they are also bad enough to limp-call especially in position.
On the flop you essentially have the nuts, since if someone had AA or QQ, they would almost certainly have raised pre. Sure you see the occational limp "trap" with especially AA, but that is such a small part of their range, it does not matter. So the question is only, how do we get paid.
And for me I want to take the initiative here and start building that pot. Which you can do by simply leading out, and in that case I would choose a rather large size, since we are targeting hands like top pair, and bad players are typically rather inelastic with that. Or you can go for a check-raise. Check-calling is my least favourite option, because now you depend on someone else betting the turn for you.
So I would pretty much never see the turn like this, and therefore its not easy for me to analyse it. I guess, I am ok with your check-raise, because he bet this blocker kind of sizing, and the other guy just called, so it look kind of weak to me. Again as played, yes I think, you need to bet the river for value. Maybe bet enough to put BB all in, and then make a decision, if the other guy come over the top.
Overall I dont think, you missed all that much value, because it was a limped pot, and the flush coming in on the turn was not, what you was looking for. But I do think, that in the long run you want to change that flop line and not go for a passive check-call, when you know damn well, you have the best hand, and you are out of position.
This is especially the case in limped pots, because noone has shown willingness to take control so far, so you typically can not depend on someone else to build the pot for you.