You know they sell that glass cleaner for your aquarium that is supposed to be safe for it. I don't think that is worth the time or money. I thought about it and the best glass cleaner(cheap and homade) you can make is made from white viniger and ammonia mixed in water.
I personally just use water, but i got glass aquariums.
However, Idont see how these two chemicals, if they got into the aquarium in small ammounts, would damage anythign in the system.