I suspect that Plantation are the best of the operators in the area. They have high quality (very stretchy) 5mm wetsuits where the others use 3mm plus pool noodles to make up for lack of buoyancy (you need to be buoyant to float horizontally without moving much). We were warmer and managed to stay in the water longer as a result. The staff were fantastic too - I was impressed with them versus the other guides that I saw. Facilities were perfect - good facilities at Plantation resort, clean boat, towels, drinks provided etc.
Apparently early morning is the best time, so we got up early for the 06:30 cruise. We also went with the small group option, which was probably worth it, although in practice, other groups of people with other guides tend to come into your group's space if there's something to see, so maybe if doesn't matter that much.
The manatees were amazing - very highly recommended. I was initially concerned that we were abusing the poor animals, but we were left with the conviction that tours such as these have been critical to their increase in numbers. The industry seems well controlled, and manatees are left in peace in marked areas Where they do interact with humans, it is only when they themselves want to through their natural curiosity. People in tour groups seem to stick to the rules. I don't know if the same is true for individuals traveling there on their own.