I'd recommend ferries

We used ferries to see Croatia and have now gone on 2 Carribbean cruises. I don't think I'd ever want to use a cruise to see cities I was actually excited to explore.

Ferries will get you closer to where you want to be on the islands and you won't have to wait in the long shuttle lines back and forth. It would also provide flexibility if you'd like to spend more time in one place or see something outside of a cruise group.

You'd certainly have to do a lot more planning on your own and paperwork than just paying a cruise line to do it all for you. So it might depend on if you think the planning of a vacation is a big part of the joy of a vacation.