We went with Byrd's Underwater because they head out the earliest (and coldest - brrrrrrr!) in the morning and you can see the manatees without crowds. You really have to do this on a very, very cold day to have a great experience and see lots of manatees. The day we went out it was in Jan-Feb and was 31 degrees and pitch dark when we arrived at the dock.
It was a great experience, but probably the coldest I have ever been in my life. It took a hot bath, breakfast and a long nap before I was fully recovered.
We took our own wetsuits and borrowed caps, but we went barefoot and that was a big mistake. The boats have thin indoor/outdoor carpet over a metal deck and our feet really, really froze. Wear the booties.
Take an underwater camera for once it starts getting light.