WOW, those are pretty darn interesting to say the least. I did a screen shot in case they disappear.
http://www.dod.mil/pubs/foi/newyorkcityflyover/Air_Force_One_supporting_documents_Part_1.pdf
Page 88 & 89
Gen Meenan questions Scott (the planner in this email trail) on Sat April 25h. Says NY populous can be sensitive to low flying planes due to 9/11.
Reply is that they (PAG) have been concerned about this and as a result have done substantial coordination.