This is more like a comment than an answer, but I have insufficient rep to comment. I think the short answer is that we lack the data to say for certain. And it definitely does depend on what compounds and contaminants you're looking for, as well as your definition of "clean."
In terms of the compounds that were marked as toxic or dangerous in previous decades, the EPA and other organizations have been working steadily to decrease their levels, so in that sense the lake is much cleaner than it was. But there are many, many, compounds in any body of water nowadays, many of which we don't have great data for. You have to test specifically for a contaminant to know how much of it is present, and when you start thinking of all the thousands of compounds that go down the drain every day....we would need a lot more tests. And even if we do the tests now, we wouldn't have past years of data to compare to.
And certain water issues complicate matters. Zebra mussels are great for making water look clear and "clean" - but they are extremely invasive and horrible for any ecosystem invaded by them. So authorities may chlorinate sections of lakes or rivers to kill them. Obviously in the short term that causes an issue with the water having too much chlorine. Another issue is the fact that a normal non-polluted lake would still have things like algae and bacteria hanging out in the water. People would think of that as "dirty" compared to drinking water, but it's pretty "clean" in terms of ecology.
This webpage from the Great Lakes Commission (and the US EPA and Environment Canada) has some great information about the difficulties of measuring the cleanliness of Lake Ontario: http://www.great-lakes.net/humanhealth/lake/ontario.html
And here's the EPA reports on Lake Ontario: https://www.epa.gov/greatlakes/lake-ontario
