Win an exchange vs winning a piece I'm black. I took the rook and ended up winning the game. Did I make the right choice? Instead of winning a bishop, and after queens are exchanged, i would have got tripled pawns.

The Lichess engine says to take the bishop, then Qxc6 Bxf1, but I'm not convinced by that line. I mean, everyone would save the rook, as mentioned above. I think if I were to take the bishop, queens would be exchanged and white would save the rook.

And says if I took the bishop I'd have 3.6 points advantage, whereas taking the rook is 0.4 only. Again I'm not totally convinced by engines so I'm asking humans. I don't like having tripled pawns. Maybe the computer approach is best, but I don't think humans would play what Lichess suggested.
It is a typical beginner's mistake to overvalue the importance of having a good pawn structure. A friend of mine once gave a whole piece away to avoid getting doubled pawns, and you argue similarly in this position. That is very understandable if you have just learned about hanging, isolated and doubled pawns and want to adhere to this newfound wisdom. 

BUT: It is very, very rare that an advantage in pawn structure is worth a full piece. The disadvantage from having doubled or even tripled pawns usually varies between zero and one pawn. 

General advice: Don't worry too much about structure or pawns in general, having active pieces is much more important. Also: Having more material is more important, if only because a piece that your opponent doesn't have, cannot become active.