Hey John, sharks are going to be an issue everywhere on the coast, but if you think about the percentage of divers with bloody fish on stringers that get attacked, its pretty low. Your feet in the water MAY be an attractant, but I used to do a lot of wading in waters with sharks and I've only been bumped once, when I was swimming at a beach when I was young. My father has been wading alligator-infested waters for years. While it scared my mom and we've both hooked into gators while fishing, these are just possible statistics-makers you have to run through your head. There will be some sort of apex predator in whatever water you are in in FL, and I mean this in the most positive way possible (as in, they are always there, and the issues are pretty low).
I am originally from Sarasota on the West Coast, so I can't give you specifics but I can give you some general ideas. If you can find oyster beds, specifically with rays cruising them, you will find redfish. If you find grass flats, you will find trout and redfish, along with other species which can give you some tight lines. Target the mangroves, as well as illuminated docks at night, for snook. These are just the basics.
Just as an interesting aside, one of the most productive shark fishers in our area used to fish out of an inner-tube. I haven't heard of any veteran fishermen in the area dying from shark attack lately so I'm sure he's still kicking around out there (literally). So you should be fine in a pontoon