Most of the waters of Crystal River is a Federal Wildlife Refuge for the protection of Manatee. Not controlled by the State of Florida. Swimming with the manatee is allowed.
http://www.fws.gov/refuge/crystal_river/ I would rent a kayak, the time of year your going you will find manatee all over. By suggestion for a kayak rental is
Crystal River Kayak. You paddle a short distance from there docks and you at Three Sisters Springs. There you can paddle into the springs and get out of your kayak and swim with them. The average count last winter was close to 600 manatee in the Crystal River Refuge.
http://crystalriverkayakcompany.com/