Booking yourself, even if the same tour/activity can be both cheaper and a better experience. The main one I remember was on one of the islands, you could go jumping down waterfalls.
We booked with a private company, got picked up from the pier, driven to the start point, went down about 25 waterfalls in total. When we got to the last 8, there was a big line of people waiting to start/take their turn. Since we were already on the 'course', then our group automatically jumps to the front of the line just getting started.
So, the big line of people were the cruise ship bookings. They only did the last 8 waterfalls, whereas we did about 25. They were in a big group with probably a lot of waiting.
Our only waiting was when my wife would hesitate at the top of some of the waterfalls.
I also believe ours was also cheaper.