I've been photographing manatees in and around Three Sisters spring every winter for the last 6 years. I just made a trip up there for the first time since the new laws went into effect last Nov. All I can say is all my images and footage from the last 5 years has just increased in value by multiples, because to reproduce the best of them would require one to now risk a huge fine and/or a federal lock up. You will have to risk a big fine to get high quality low angle underwater shots in there. There is no legal way around it, even by permit.
The reality of the new law:
Note that the new law isn't really against scuba, it's against diving in any form. You cannot dive down to a manatee even on snorkel or if you're buck naked. The law is worded to say any harassment is punishable by fine and/or imprisonment. Then it goes to define harassment as anything that alters the behavior of a manatee. It goes to include harassment as 'diving down on to a resting or feeding manatee'. Carefully note this is worded "on to" not "onto". Now here is the practicality of this enforcing this particular statute. The US Fish and Wildlife officers (now stationed like storm troopers around the spring) are not in the water, and have no intention of ever being in the water. If you dive down, they can't see what you are doing, so they need to suppose you are diving down on to a resting or feeding manatee. You will be told by the tour operator or boat rental shop FIRMLY and REPEATEDLY that you need to keep your head above the water at all times, or risk a Federal fine. You can put your face in the water, but your head can't go below the surface. If you think I'm kidding, take your DSLR camera into Three Sisters and you'll see you'll attract more attention from the 'law enforcement' people than a mut hound does fleas.
What I found very ironic was that even though harassment is defined as anything you do that alters the behavior of a manatee, this apparently excludes kayaks for now. My police officer buddy and I witnessed several occurrences where a manatee trying to enter the narrow spring run actually backed up and aborted its attempt to swim up the spring because of an armada of kayaks lined up overhead trying to exit the spring. At one point, there were 10 kayaks lined up trying to exit. (go it all on video.) This obviously constitutes harassment by the definition given by the law. I expect big changes to specifically regulate kayaks is coming next year.
FWIW, I used to shoot in Three Sister's on scuba, and would calmly sit in one place while manatees would approach me and check me out out of curiosity while masses of snorkelers and kayaks chased them around at the surface. On one instance, I had a manatee come up to me and put his eye repeatedly up to my lens to see what it was. Apparently he was seeing his reflection. Made for a great experience and equally great images. Glad I was able to do so while I could. If you still plan to try your luck, I suggest you learn to hip shoot or shoot blind by holding your camera as far as you can underwater, angled up to attempt to pull off a low-angled shot.
Best regards,
Brian