Surprising you didn’t get a lot of replies, usually people are good about giving suggestions. I stopped by your topic to see what others would suggest as I was curious too. I’ve been told that the cruise ship will not accommodate you if you don’t book thru them and something happens that you get delayed returning. Correct or not you need to check. Also, while researching my own cruise (didn’t end up taking it) I found that everywhere a cruise ship stops you can google dive shops or dive trips and you will get several hits every location. I was picking the dive boats that said right up front on their ad that they catered to cruise ship divers. After going in they would stress that either they were right at the dock or they picked up and dropped off at the dock and they gave you the time of dives. Also these tended to stress that they were not cattle boats and several gave you their undivided attention. Might they be a little more then what the ship has to offer? Does it matter versus a good time? Do you then need to ask on here (hopefully get responses) and google their shop to check on negatives? Orrrrrr,,,,,,,, you can just tell the ship you want to dive every location and let them handle it.
Inspite of all that, I hope you have a great time whatever you do! (Wish I had this dilemma!)