Another comment mentions Zebra mussels, which have made the lakes quite a bit clearer in recent years (but not necessarily to good effect).
I don't know about Lake Michigan, but I wouldn't really have advocated swimming in the parts of Lake Ontario I was around in the '80s.
And anyway this is a seasonal effect brought on by a larger than usual ice content this past winter. If I read the article correctly this won't last long and run off from surrounding farms and industry will have the lake algae ridden and opaque before too long...
And it looks like the evidence for run off causing algal blooms in the Great Lakes is pretty convincing.
Fecal matter from birds--like the scads of corrmorants around Kingston--is rich in nutrients, and while agricultural runnoff can be a problem Lake Ontario doesn't suffer from it particularly, and even without it there are plenty of altnernative nutrient sources.
I think a city's relationship with its waterfront has to do with what was built on land next to the water. In Toronto the lakefront was industrial until recently. In Chicago the industry was clustered along the river and the lakefront has consisted of parks and beaches for a century.
This sounds made up, but my father worked for the state department that oversaw municipal water treatment (as a civil engineer, many cities on Lake Michigan draw water from the lake), so I guess I would have had some awareness of serious issues with the water.
Aside from the detrimental effects on local species it also means that algae and weed blooms are common and it's not uncommon for harbors to be choked with weeds by August.
Not sure if all the current water clarity across the lake can be attributed to them but the change inshore has been rapid and remarkable.
This was on the western (Wisconsin) shore of the lake, though, which may have been colder due to upwelling from the prevailing westerly winds.