Yes, but sort of meh - most, if not all, surface waterbodies in developed areas are "polluted" in some degree of the term. Even Lac Tremblant is "polluted" by gasoline and oil from motorboats, fertilizer, etc. but even those in otherwise "pristine" areas can be polluted (i.e., some small lakes in the high adirondacks near Lake Placid have been impaired for decades due to acid rain deposition from pollution in the midwest). The fact that your link lists the Mississippi River and starts with the fact that its brown, is not a great indicator of this list's credibility...sedimentation and turbid water is often a natural phenomenon, it is not a direct indicator of pollution. The fact that the Hudson River isn't on that list should be a good reminder that stuff like that is very subjective. I sort of couldn't restrain myself there because I work in the environmental field...lol. So yes, that's a legit claim, but I don't think its fair to say CHOO is "polluted" and all/most other swims aren't. A coastal ocean swim in an otherwise "clean" area, a day or two (or three+) after a heavy rainstorm - depending on the area's sewer infrastructure - can easily be many times "worse" in terms of pollution and human health than a swim in the TN river.
This all being said - I agree with you that CHOO getting #1 swim is really weak. The fact that it's current-assisted seems to overrule every other factor that makes a swim "good", and I don't agree with that. I haven't done all these races, but I'd say LP, MT, and Canada all are head-and-shoulders above CHOO in terms of overall swim quality.