I've found that the snorkel trips with a stop on Caye Caulker don't give me enough time on Caulker.
I guess it depends on your priorities, snorkeling or hanging on Caulker.
I think the Lady Leslie trip gives you around 2.5 hours on Caye Caulker. That's enough time to eat lunch, have a couple of drinks, walk around some, and do a little shopping (there are several nice art galleries, all small). But if you want to hang at the split, sunbathe, spend all afternoon at the Lazy Lizard, you'd be better off with the ferry option and saving the snorkeling for another day.
All depends on what you're looking for. We're not sunbathers so like the snorkeling trips best.