The New York Times beat La Nacion, NPR and the Boston Globe to the 'large' award for General Excellence in Online Journalism, while AxisPhilly, a non-profit news organisation based around Philadelphia, and The Texas Tribune were commended for their work in the small and medium categories.
The Guardian's ongoing work in revealing the NSA files leaked by Edward Snowden was commended in two categories, the Gannett Foundation Award for Innovative Investigative Journalism and the Gannett award for Watchdog Journalism.
"They got the most important story of the year and they told it well," said Joshua Hatch, chair of the Online Journalism Awards, quoted in the Guardian. "This was a combination of most important and told well. That's a tough combination to beat."
The Boston marathon bombings featured twice in the breaking news category as the Boston Globe and Boston University News Service picked up awards in the large and small sub-categories.
"The public craved information during the dark hours of that long week, and the newsroom of The Boston Globe responded to the absolute best of its ability,” editor Brian McGrory was quoted as saying on Boston.com, which shared the award with the Boston Globe.
The Boston Globe also received the Knight Award for Public Service for 68 Blocks, an online package of multimedia content and stories surrounding the Bowdoin-Geneva neighbourhood, one of the most dangerous areas in Boston.
A full list of winners can be found on the Online News Association website.