The springs have clear water, the bay won't have clear water. However, the springs will get murky if people are standing on the bottom, so pick your poison. Go wide wide wide and the murky water won't be that bad.
Strobes allowed after the sun is up, I think they want you to wait half an hour after sunrise. Try to minimize your power and number of shots taken, these guys aren't on a nice model contract, they are posing pro bono...
There is also Kings Spring. My advice is, go out with Birds Underwater. Their boats run 1 trip a day, and they leave early. It's nice to still be out on the water as you watch the other boats leave, and return with other loads of people. And, by waking up early, you get out early, and get to see the manatees alone.
You aren't supposed to go completely submerged, but with a wide angle lens, you really won't have a problem, just hold it below you and shoot up if you want to.
They do have a ton of rules about touching and harassing the manatees. Follow all of the rules, especially the ones about the manatee zones and staying out of them. They do have people watching and you will get fined. Birds stresses this a lot.
You can rent your own boats, but I wouldn't rent anything but a kayak. With a motor, you have to be so careful not to hit a manatee.