The FAIR Media Bias Toolkit provides tools you can use to evaluate an entire publication or website:

Before you dig into a story too much on your own, see if someone else already has. In the open textbook Web Literacy for Student Fact-Checkers, Mike Caulfield identifies the following organizations as generally regarded as reputable fact-checkers for general U.S. news:

By IFLA (http://www.ifla.org/publications/node/11174) [CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons