Cayuga Lake is hard to talk about as just one ecosystem, because it has such a strange set of features... It is (like all of the Finger Lakes) a collection of water in the bottom of a glacial valley. Unlike many such lakes, however, Cayuga lake is VERY deep in places (over 400 feet deep), and there are (if I recall correctly) springs or caves or something like that at the bottom in the really deep parts. That being said, it also has a decent sized shallow shelf, and a bunch of small bays and swamps where various creeks discharge. It's the shelf-like area at the south end where the cooling intake and outlet pipes are.
Much of the difficulty assessing whether the heat being pumped into the lake was going to have any negative impact or not had to do with the constant protesting by massive numbers of hysterical but scientifically illiterate hippies (if you've lived in Ithaca for a decade or more, you know who I am talking about). As sad as it is, because anything Cornell released or published was decried as bunk if it didn't damn the project, it didn't seem to matter any more what (if any) case they made to the community as a whole, so there wasn't much effort after some point to communicate anything clearly about this project. I don't blame them, it must have been like trying to piss out the sun getting those damn hippies to shut up long enough to have any sort of rational discussion.
In any case, I doubt it has done nearly the harm that the late '70s and early '80s did when the city essentially pumped any excess sewage right into the lake with minimal if any treatment. In any case, I think a heat tax would be a good idea, but only if it were absolutely universally applied (Apply it to residential, commercial, public sector, and industrial waste-heat and in some sort of a meaningful and constant form (X cents per Y million Joules)).