For a decade in the 1980s, Alter was Newsweek's media critic, where he was among the first in the mainstream media to break tradition and hold other news organizations accountable for their coverage, a precursor to the role later played by blogs. When Newsweek launched his wide-ranging column in 1991, it was the first time the magazine allowed regular political commentary in the magazine, other than on the back page. After the election of Bill Clinton in 1992, during which Alter was a consultant to MTV, he was among a small group of reporters and columnists who had regular access to Clinton, though he was far from a reliable supporter, particularly during the Monica Lewinsky scandal. "Alter bites me in the ass sometimes, but at least he knows what we're trying to do," Clinton was quoted as saying in the book Media Circus by The Washington Post's Howard Kurtz.

In late 2001, in the wake of 9/11, Alter wrote a column backing certain kinds of torture, arguing for the implementation of a psychological torture program in the U.S., as well as having prisoners in American custody shipped oversees to be tortured more severely elsewhere. Alter later regretted the column. "There is one column I'd very much like to have back--a column that to this day makes me freakin' wince at the thought of it. This column was not technically inaccurate, but it was still a mistake--a big mistake--to write it."

Alter became a sometimes fierce critic of President Bush, with a particular emphasis on what Alter considered his lack of accountability and his position on embryonic stem cell research. Alter, who is a cancer survivor, has written and spoken occasionally about his own bout with lymphoma and experience with an adult stem-cell transplant. On NBC's Today Show, Alter was the correspondent for several stories about the effect of the Iraq War on returning veterans. The Defining Moment, which was reviewed respectfully, surprised some critics with its analysis which concluded that the States had come very close to dictatorship before Roosevelt became president, painting him as the savior of American democracy and capitalism. During an interview with 60 Minutes on November 14, 2008, then-President-elect Barack Obama said he had recently been reading The Defining Moment and hoped to apply some of Roosevelt's strategies that were outlined in the book into his own administration.

In 2009, Alter was the commencement speaker at Western Connecticut State University, which awarded him an honorary doctorate. He also has received honorary degrees from Utica College (2008) and Montclair State University (2009).

He lives in Montclair, New Jersey with his wife Emily Lazar, a producer of the Comedy Central show The Colbert Report, and their three children.