That report was written almost 300 years later... Things can change drastically in a fraction of that. Also, I think we can all agree that the quality of life of the natives got increasingly worse after the arrival of Europeans (along with European diseases). If the quality of life, health, mental state, etc... has an impact on stature I'm sure 300 years would have made quite an impact.
I would agree, but to a much more modest extent. For instance, today, in 2013, the average man is 5'9." A hundred years ago an average man was a little over 5'8" (interesting page). So in the past century the average male has grown around 1.5" taller, which is a noticeable change but nothing astounding. It's interesting that the average prepubescent child today is a lot taller than his or her equivalent a century ago, but growth tends to level out at around age 21. Given these facts, I rather doubt that any population of humans has grown or shrunk in the past several centuries by two or more feet.
Dr_Acula, have you contacted or researched the collections of the Smithsonian? This is the largest holding of skeletal human remains in the Western Hemisphere, if not the world. What information might they have?