A wonderful place to park and see manatees for free is the viewing center at Tampa Electric. On my first visit I walked onto the boardwalk and was surprised to see all the big boulders in the water. Then I realized they were the manatees. There is no underwater viewing window (or at least there wasn't when I was last there) but there are LOTS of manatees to see just looking down into the water.
Here's their website:
Manatee Viewing Center - Tampa Electric