The annual George Polk Awards in Journalism, which honour special achievements in the field, were established by Long Island University to commemorate George Polk, a CBS correspondent who was killed in 1948 while covering the Greek civil war.
Hastings' piece, "Runaway General", which received the magazine reporting award, resulted in the sacking of McChrystal by Barack Obama.
Rolling Stone drew criticism from some media commentators after deciding to hold back the story for its print edition rather than make it available online.
Other winners of the awards include the Associated Press in the environmental reporting category for its coverage of the Gulf oil spill. Both the New York Times and non-profit news organisation ProPublica received two awards each, the latter for collaborative projects with other outlets.
"After a drought of several years, a number of major metropolitan newspapers produced significant investigative work during 2010," curator of the George Polk Awards John Darnton, said in a release.
"And for the first time, there were some truly noteworthy collaborative projects across print, television, radio and the Internet."
The awards will be presented to the winners at an event in Manhattan on 7 April. According to the release Associated Press correspondent and former CBS News reporter Kimberly Dozier, who was seriously injured in a car bombing in Iraq in 2006, will be the citation reader.
A full list of the winners and their work can be found here.
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