Professor Woods addresses this question in his book, 33 Questions You Aren’t Supposed to Ask about American History. Essentially, from what I remember, Congress did pass a resolution acknowledging the contribution the Iroquois Confederacy had on the US Constitution, but Dr. Woods says that the Iroquois nation had zero influence on anything that went into the Constitution. I believe all that is mentioned during that period is a letter written by Benjamin Franklin stating that if the Native Americans could form a Confederacy for their defense, then the Colonies could. This, however, was during the American War for Independence not during the formation and ratification of the Constitution.
Hope that helps,