You're lucky they took you out at all in 5-6 foot swells! I was in the Keys November 15-22 and Cap'n Hook's in Marathon had to cancel 3/5 dive days due to the 3-4 foot rollers!
Can't say with the Keys but out of West Palm Beach there can be a wide difference between boats and Captains. As I understand it, some boats are more stable in higher seas. Since I vacation to dive its one reason that I switched the boat that we routinely dive from out of WPB, choosing to dive with a boat and Captain that was comfortable with sporty seas.