Over the course of Phase II and Phase III of the MCU, the Avengers renovate a former Stark Industries storage facility north of New York City and use it as their headquarters. From shots showing the Hudson River and Manhattan in the distance, I think it’s somewhere in Rockland County, perhaps near Nyack. Can anybody place it more precisely?
According to this site
As you can see from the Google satellite view, the location above matches the original photographic background plate to a ‘T’. I can solidly proclaim that the Avengers are headquartered in Esopus, New York!
For Captain America: Civil War the layout was changed slightly and the entire facility was placed into context of the Hudson River Valley. According to Cinefex #147, an aerial plate was shot of an actual plot of land along the Hudson River. Effects artists then placed the buildings into that plate. When I first saw the image of the plate from that issue, I thought it would be impossible to find the actual location.