Their total circulation, along with a few local independents, is less than 500,000 -- "a drop in the ocean" of Russia's potential 143 million readership, says Alexei Simonov, president of Glasnost Defense Foundation in Moscow.
Former Soviet leader Mikhail Gorbachev, a 10 percent shareholder in Politkovskaya's newspaper, called her murder "a blow to the entire democratic, independent press."
The paper has offered a reward of nearly $1 million for information leading to the capture of her killers and whoever ordered the murder.
"There has been no deterioration" to freedom of speech in Russia since Putin came to power, Vladislav Surkov, the deputy chief of the presidential staff, told reporters last month.
Supporters of the Kremlin blame any criticisms of their government's handling of the media on an anti-Russian bias in the Western press.
Putin has not publicly addressed the Russian people about the murder, a move that has fueled resentment here.
The day after Politkovskaya's murder, hundreds gathered in a central Moscow square to express their outrage at what they said was the government's lack of response to the killing of one of the country's best-known journalists.
The Kremlin released a statement on Monday stating that Putin had assured President Bush in a phone call that the country's prosecutors would bring Politkovskaya's killers to justice.
At a meeting with German Chancellor Angela Merkel in Dresden, Germany, where Putin once served as a KGB officer, the Russian president called it an "unacceptable crime."
"Her influence on political life in the country was extremely insignificant in scale," Putin said.
Putin went on to say that the public fallout after her murder had done more to harm the reputation of Russia than the critical articles she wrote about the current regime.
Her followers took offense to his comments.
"If her stories weren't dangerous, she wouldn't have been killed. There wasn't anything else to kill her for. This means her stories carried weight," said Gutiontov of the Russian Union of Journalists.
Politkovskaya's reports on the atrocities of Russia's war with the southern state of Chechnya won her numerous international reporting awards and enemies.
This week, Novaya Gazeta published the report she was working on before her death. The report detailed alleged torture by Russian security forces in Chechnya.
She said that she had received several death threats.
In September 2004, she suddenly fell ill after drinking tea on a plane as she flew to cover the school hostage siege in Beslan.
She later said that she had been poisoned to keep her from covering the event.
"You can't do what she did here in Russia. You just can't without finding trouble for yourself," said Nina Shumilina, 56, a doctor in Moscow. "She was probably too brave."
Who, if anyone, will follow in her footsteps remains to be seen, and they will have to wear big shoes.
Politkovskaya was the third journalist from Novaya Gazeta to be killed since the breakup of the Soviet Union in 1991.
"No one can do it like she did. But we'll try to work harder as she's no longer with us. I am sure the journalists haven't surrendered to intimidation," said Lyudmilla Alexeyeva, the head of the Moscow Helsinki human rights group