My DD has been doing these cruises since she was four years old, once or twice a year. She has done all four of them, some of them multiple times.
Albatross Treasure Cruise - Yacht Club ...she loved this one. It seemed to have consistently energetic CMs who really got into character. She also liked going into the World Showcase before it was open. Having the YC's lighthouse and Stormalong Bay's shipwreck in the background make for a very nautical feel, which added to the general atmosphere. This was her favorite of all of them.
Bayou Pirate Cruise-Port Orleans ...this one went to Downtown Disney, which was nice, but allowed for less freedom for the kids as they had to be very closely supervised. (Not that I wouldn't want them to be very well supervised, but going to such a public location, they had to be in a single file line and all. She enjoyed the illusion of freedom that she got with the other cruises more, as they searched on pretty much deserted resort beaches.) It seemed less "Piratey" than the others. She only did this one once, and the treasure was in the lobby at the end of the cruise, which seemed odd. It might not always be that way.
Grand Floridian offers the Captain's Shipyard Cruise ...this is the one she has been on the most times, just because it was convenient to the Magic Kingdom and so easy to get to. The CMs have always been enthusiastic. It's her second favorite, after the Yacht Club. They go all around the lake, making stops at the CR, Poly and GF beaches.
Island of the Caribbean Pirate Adventure ...this was super-convenient when we were staying at CBR. We wouldn't choose this one if we weren't staying there. It covers the smallest area, being confined to the resort's lake, and was the least fun, according to DD (probably because I could so easily follow her around lol). I could see her pretty much the entire time, so for parents of younger children it might be a good option, as you can follow the boat around via the pathways and keep it in sight.