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.
This June, I went to Bonaire as part of the Scubaboard Invasion. Dennis has been telling me for years I should attend, but this was the first year it worked out for me to go. The Invasion was amazing on its own, but the best part was spending almost an entire day underwater, on dive sites all around the island.
I know a lot of people go to Bonaire for shore diving only, but the Invasion deal included morning 2 tank dives, so I was able to dive Klein Bonaire as well as some of the more difficult to enter shore diving sites, then go out in a rented truck in the afternoons. Both types of diving were enjoyable.
Additionally, Sola was there with their Nightsea lights, letting people borrow them. They aren't cheap, but for anyone who dives at night, the effect is incredible. Because they have a white filter, these are perfect for anyone who dives at night. Just put the white filter on the front if you need to see white, otherwise, I was surprised at how easy it is to dive for an hour in the dark with only the black/blue light on.
I do mostly cave diving photography, and I get this when divers face their bright HID primary lights (or LED or whatever technology...) at the camera.
The light comes in and reflects off the front of the lens, which then bounces off the inside of the dome and back into the sensor, showing up in my pictures.
Some people take thin velvet type fabric and put it on anything on the lense that's not part of the glass optics, but I also don't like bright lights blowing out the image so I just train models to shine their light to the side, and it gets rid of it most of the time.
The 2nd method is the better one. You don't need a monkey wrench, get the right size wrench and guard it with your life.
Get it nice and long, and apply a slow even pressure.
Don't put the valves on with very much pressure. Some say hand tight is right, but I think the proper torque is a bit more than hand tight. Also, use Cristolube or Tribolube on the threads of the valve when putting it back in the tank. You don't need a lot. (I think you could use silicone grease as well, if you aren't using anything but air in the tanks. Personally, I prefer to avoid it anywhere near my breathing gas)
Breaking valves is a sign that you are putting them on too tightly, and probably getting some galvanic corrosion between the threads of the tank and the valve.