Most of these solutions are vastly underestimating the resilience of a large city's industry, even if you assume that the city's casters have not been taking steps to deal with this kind of thing. Minor terrorist actions like planting some explosive runes around the place will serve to do little other than get your characters hunted down and killed - and likely the city's military and industrial factions will use your actions as an excuse to tighten security and cut equipment costs, likely increasing the extent of the problem you are trying to solve.
If you don't wish to solve the problem via the tried and true "Quest until the DM says you win" strategy, and killing everyone in the city is out, your main options are probably economic - providing a cheaper, cleaner alternative to the products the city is producing might work, although if the real world is anything to go by even that is chancy at best, as older, inferior products triumph in marketing over newer, superior products all the time thanks to social inertia.
In that case, your best bet is probably some kind of magical effect that will make industry impossible - something that will render the city uninhabitable non-lethally like constant, pouring rain. A permanent weather control effect might work (Although bear in mind that even that will probably kill hundreds or thousands of people in the ensuing floods, famines, and refugee flight). archangel.arcanis has a good idea with the plant growth, but non-permanent effects will pretty much just be shrugged off (for proof of this, look at how quickly real cities both now and throughout history have recovered from disasters of even truly staggering magnitude) - and if it's something you have to renew, you are likely not to be able to, thanks to retribution from the law.
Bear in mind also that displacing the industry from this city without addressing the underlying economic forces that make this kind of industry profitable is an extremely short-term solution: even if you destroy this city wholesale, demand for those products won't go away, and their manufacture will just move elsewhere. Essentially, the two of you are undertaking the problem that environmental groups worldwide have been struggling with unsuccessfully for some hundred and fifty years. Now, in a game world, you have more tools available to you (the strongest, of course, being the Power of Plot), but if your DM wants to model this action realistically, be prepared to find that there is no instant, easy, one-shot solution.
tl;dr: You need to make the city's industry impossible or clean forever with a single action, or you will accomplish nothing, and historically, the only ways to make industry impossible are to destroy everyone in the city or remove the economic incentive for that industry to exist.