Theoreticaly, you can. But most naturally ocurring whirlpools in the rivers are way too small and have way too little power to be a viable large-scale solution, nevermind other potential issues such as freezing water in winter, debris, trash, etc. The big powerful ones in the oceans have the same issues as other existing marine technology, namely expensive and difficult installation, high maintenance and repair costs, challenges related to the bottom surface, gravel, sand, salt, corrosion, debris etc. Whirlpools in oceans are also highly dependent on the tides, so it's not a very stable source either.