1hr 7 min 2 sec
1hr 20min 43 sec
There is a New York Nights movie from 1994 that has the WTC on the poster
Let It Be Me (1995) poster
The 2018 Johnny Depp film City of Lies has the WTCs at 4min 55sec
Blue is the Warmest Colour has the WTCs at 2hr 32min and again at 2hrs 46min. If memory serves, its just a photo of the NY skyline in the background as the whole film takes place in France.
*A Beautiful Day in the Neighborhood
Times are rough estimates as I saw the movie in theaters and didn't have a time stamp.
I've also heard that the documentary about Mr. Rogers (Won't You Be My Neighbor) talks about 9/11. I've never seen the movie myself so I can't confirm or give you any times.
*King Kong (1976)
Shot of WTCs at 1hr 42min and 1hr 43min
Shot at 1hr 20min