The Empire State Building was hit by a B25 Flying Fortressmany years ago. Read about waht happened, and no it it did not crash to the ground. http://www.withthecommand.com:80/2002-Jan/NY-empireplane.html
Remember, that's a B25, not a B52 (a mistake made by the makers of Loose Change). The B25 is a small/medium sized twin-engine bomber. I would not expect any skyscraper to be taken down by an aircraft that small.