There is now a lot of contamination of water in the areas flooded by Hurricane Irene and subsequent storms. We own land on Batavia Kill near Windham and Prattsville in Greene County, NY. Normally this is safe to drink, but raw sewage, oil, gasoline and other contaminants were swept into the stream. I've seen one picture that shows the house and foundation and most of a yard washed away; this includes the whole septic system except the tank. I've also seen pictures of roads washed away leaving raw sewage flowing into a stream from a broken pipe. NY and VT are recommending that wells be disinfected in the flood areas. So, even if you believe that you don't normally need to treat water, in the Catskills and Vermont I'd say treat even at 3000'. If wells are contaminated you have to wonder whether springs at some distance from the contamination sources could be contaminated, since they are presumably drawing from the same aquifer.
I wouldn't drink even treated water from lower elevation streams in Catskills, ADK or Vermont until any contamination has washed out; I have no idea how long that takes.
The article you site shows measurements at the outlets of large reservoirs. My recollection is that this is the safest place to draw water -- the water leaving has been disinfected by UV from sunlight and any contaminants are very diluted. Streams and springs might have a very different result.
Bacteria are probably a more likely cause of illness than Giardia (no references for this).