Based on the advice of some kayakers I met in Crystal River (the same ones whose fervent praise of my kayak almost made me blush) I decided to visit Rainbow Springs which is about 45 minutes north and east of Crystal River. I camped the night at the state park of the same name and then launched the kayak from their launch point (you can also launch at nearby KP Hole Park which is just across the river.) I paddled upstream a little over a mile to the headspring. The waters were, if anything, even clearer than those at Three Sisters Springs and often reached over twenty feet in depth in the deep pools where the aquifer feeds the river. I saw numerous turtles and river otters as well as countless birds.
A short video of me kayaking at the headsprings: