There are many places to view manatee throughout Florida, but I will focus only on places where you can get up close and personal. Mainly winter is the best time of year to find manatee in large numbers. As the days and water get colder, the manatee travel to many of Florida's fresh water springs where the water is an average of 72 degrees year round. They gather in groups this time of year.
As I mentioned earlier Crystal River is one of the best places. There are a couple of primary areas where the manatee hang out, Three Sisters Spring & Kings Bay. It is best to arrive at daybreak or as early as you can. Dive tours usually meet around 6:30am for a 2-3 hour trip. Myself, I rather rent a boat and make a day of it.
Another great place is
Blue Springs in Orange City, Florida. (less than an hour north of Orlando) Here the manatee come up each winter into the warmer spring water. Typically when the manatee begin to show up, the swimming area is closed. You can view them from the dock. However, divers can still enter the "boil" and snorkel around where some of the manatee may approach. Again I will emphasize that you are not to swim towards a manatee, but if they are willing they may come to you. REMEMBER - Look, but don't touch.
Finally, Homosassa Springs
claims to have manatee to observe at close range 365 days a year. The have an exclusive floating observatory where you can go below the water's surface to view the endangered marine mammal.
Great viewing locations:
Crystal River National Wildlife Refuge
Blue Springs State Park
Homosassa Springs State Wildlife Park