With mega-corporatization, there is obviously going to be astronomical amounts of pollution, more than there is now, even with fuel-cell cars. At the same time, there are crazy magical ways of cleaning up pollution at rates that are much, much higher than before. What I'm wondering is, who's winning, the polluters, or the cleaners? The cleaners can grow forests and destroy world governments; the polluters have extraterritoriality. Considering the path of history, with awakened groups and ethnicities consistently utterly destroying entrenched technocratic interests, (Ghost Dance, Yakut, NAN, Amazonia, even Imperial Japan) how can the polluter's be winning? And considering that this is cyberpunk, with all the gloom and doom and all, how can't they be?

By the feel of the setting and nothing else to back me up, I'll say the polluting megacorps are winning.

Even though every government collapse (UCAS, Russia, All of South America, Australia) has been the work of massive magic usage? I guess that works for me.

Hmmm an equlibrium, very interesting.

In terms of clean places you have Amazonia, Siberia (which is in a low hostility conflict with Russia, not exactly an environmentally friendly activity), the NAN (which includes Tsimshian, the two anglo stink bombs Seattle and California, and some of the old US nuclear testing sites), the two elven nations (both rather small geographically and so of little concern), and I believe Switzerland and one of the fractured nation states of China (which also contains radioactive testing areas).

In terms of unclean places you have pretty much everywhere else. The non-NAN parts of north america, especially the UCAS, are pretty bad. South of the border Aztlan is pretty nasty as well. Much of europe and england are messed up, especially around the north sea which is a toxic sludge pool. Japanese megacorps are no doubt carefull in their own homeland but I doubt that applies anywhere else, especially since much of southeast asia was once their colonial playground.

The clean places are enough to keep mother nature from going into cardiac arrest but they're more like a life support system than an attempt at resuscitation. Meanwhile the polluted areas continue to get nastier, and the more polluted they are the harder it becomes to clean them up. Plus there is little that eco-activists want from the polluted areas, but there is plenty that the corps (and others) want from the clean areas, and they usually end up polluting those areas when they grab what they're after.

The eco-activists winning will only happen if the eco-friendly nations move to invade the rest of the world. Amazonia is checked by Aztlan, Siberia is (or at least was) in the midst of a civil war, the NAN can barely keep itself together, the two elven nations don't really give a damn about the rest of the world, neither does Switzerland from the looks of it, and Manchuria has some ticked off communists breathing down its neck. For the polluters to 'win' things just have to continue on the way they are going.

It really depends where you are I think. On a global scale I'm going to back whoever posited the equalibrium idea. However on a local level you can do just about anything, and keep in mind that each character is going to have a different point of view based on background. An orc who grew up around Glow City might find a smaller less industrialized city to be pristine where as a tribal type from the Montana wilderness could find the same small less industrialized city absolutely filthy.

On a side note anyone ever thought about taking allergies to clean air or pure water based on the character coming from an area that has been severely polluted for mutliple generations?

I think your view on how much pollution/eco-friendliness is around is going to largely be decided on where you are at the time. Like someone else said, certain areas in the world have largely revamped their ecosystems, but a lot of other places continue to let things slide (or crash) downhill.

But this Earth is a bigger place than a lot of people can imagine. The Atlantic Ocean for example, contains untold trillions of gallons of water. It would take an immense amount of energy (or pollution) to alter the entire ocean by even 1 degree of temperature.

To use a real world example, look at the differences between a morning in San Fransisco on a bad smog day and that same morning in a small Indiana farming town. In Indiana, you would think the environment is just fine, in San Fran, you would likely think just the opposite.

Well, the Target: Wastelands sourcebook is very useful in regards to this question, as is the eco groups section of Loose Alliances

Basically, the levels of pollution in Shadowrun is EXTREME, despite the attempts of eco-activism groups and Amazonia to prevent this (or in some cases, they have made things worse).
Without strong governments to enforce environmental regulations the corps have free reign to do as they please. And that pretty much means ignoring the problem, until it starts to hurt profits to a greater degree than fixing it up will.

The most heavily polluted areas would probably be the North Sea, the SOX, Tsimshan, the Libyan desert and the Yucatan.

It's not just the Mega-Corp polluters versus the nature magicians though.
I think the deciding factor and big winners in this would be the many Toxic Shamans that the Corps would inadvertantly create.