Rolling Stone announced yesterday it had picked Tsarnaev for its August 3 to highlight a feature story about him and the attack that killed three people and injured hundreds more.
The 19-year-old issue stares out from the cover, looking much like one of the fashionable, youthful rock stars who are the magazine's usual subject matter. His appearance has been compared to that of The Doors lead singer Jim Morrison.
The picture had been posted on social media by Tsarnaev and was previously used on the front page of the New York Times.
Boston Mayor Thomas Menino has accused Rolling Stone of rewarding a terrorist with celebrity treatment, Buzzfeed reported.
"It is ill-conceived, at best, and re-affirms a terrible message that destruction gains fame for killers and their causes," he said in a letter to the magazine's publisher.
"The survivors of the Boston attacks deserve Rolling Stone cover stories, though I no longer feel that Rolling Stone deserves them."
Rolling Stone's response to the criticism was to issue a statement in which it defended the article, but not the cover.
"Our hearts go out to the victims of the Boston Marathon bombing, and our thoughts are always with them and their families," Rolling Stone said.
"The cover story we are publishing this week falls within the traditions of journalism and Rolling Stone's long-standing commitment to serious and thoughtful coverage of the most important political and cultural issues of our day.
"The fact that Dzhokhar Tsarnaev is young, and in the same age group as many of our readers, makes it all the more important for us to examine the complexities of this issue and gain a more complete understanding of how a tragedy like this happens."
That's little consolation for bomb victim James "Bim" Costello, 30, who needed pig skin grafts on most of his right arm and right leg after the bombing. His body was pebbled with shrapnel, including nails he pulled out of his stomach himself.
Three of his close friends lost legs that day and others suffered serious burns and shrapnel injuries.
"I think whoever wrote the article should have their legs blown off by someone," struggle through treatment "and then see who they would choose to put on the cover. "
The accompanying story, he said, "just seems like a cry for attention" from Rolling Stone.
Lauren Gabler had finished her fourth Boston Marathon and was two blocks from the finish line explosions that April day.
At first she thought the Rolling Stone photo, released on the magazine's website and Facebook page, was of a model or a rock star.
"All of a sudden you realise that's the Boston bomber," said Gabler.
"The cover almost tricks you into what you're looking at. I haven't read the article yet, and I know it will probably be quite in-depth, but my initial reaction is that the photo that's being used almost makes him look like a good guy."
Rolling Stone's website is prominently using a grainy image of Tsarnaev, with much less of the baby face look of the magazine cover. The website also has the headline: The Making of A Monster, whereas the words on the actual magazine cover are simply, The Bomber.
Massachusetts Governor Deval Patrick called the cover "out of taste".
"I haven't read it, but I understand the substance of the article is not objectionable, it's apparently pretty good reporting," Patrick said.
"But the cover is out of taste, I think."
At least five US retailers with strong New England ties - CVS, Tedeschi Food Stores and the grocery chain the Roche Bros - said they would not sell the issue that features an in-depth look into how a charming, well-liked teen took a dark turn toward radical Islam. Stop & Shop and Walgreens followed suit.
CVS said on its Facebook page that its decision was out of respect for the victims of the attack and their loved ones.
Tedeschi's Facebook page said music and terrorism did not mix. The company could not "support actions that serve to glorify the evil actions of anyone".