Best flyover ever in my opinion was the Bills-Giants Super Bowl right after Whitney Houston sang the national anthem. I don't know how you can top that combo, given what was going on at the time.
For me personally in terms of ones I have witnessed, the best flyover was when I was once at a game when instead of the typical squadron of fighter jets doing the flyover it was a stealth bomber. That was absolutely jaw-dropping; I can't even begin to describe that sight.
I too was there for the Jets game post 9/11 and that flyover had a sh*tload of emotion.
Was at the opener this year and was walking to my sets (300 level) right before the anthem was played. Stopped on the walkway right above Mcdonald's and the sign....could see the field. Friends were ticked at me. I said...just wait a minute....could see the fighter jets in the distance and then they hit the afterburners and flew DIRECTLY over our head - and if you recall...they were low for that game. Best place to see a flyover at Gillette is up on that walkway.