Since some commenters were curious about the Twin Towers on the Queens Museum of Art's panorama, we reached out to the museum to get some answers. The Twin Towers are currently still on the panorama, and we were told this afternoon:
They will stay up at least until the building of the new World Trade Center is complete. At that point, we will install a model of the new WTC and remove the Twin Towers from the Panorama and place them in a vitrine to be displayed in the same room as the Panorama.
The towers actually haven't been there that long, they were added when the museum last updated the panorama in 1992.