I went snorkeling with manatees about five years ago. We went to Crystal River. The company we snorkeled with was "Art N Dive", I believe. They were very informational. They took us to two separate dive sites- one in a murky river and the other in a crystal clear part, which was only about 4 feet deep. Manatees were EVERYWHERE! This company was also very much into protecting the area and the manatees. On our way to the second site, we saw a boat going way too fast, so the driver told the boat to slow down, but also called the authorities to alert them. A large school group was visiting while we were there and at the second location, a young boy (about 9) thought it was funny to ride the manatees. Once again my driver came to the rescue! My family absolutely LOVED this company & vowed to go again with them sometime!
Hope this helps!