The bookstores say Amazon and other publishers are in violation of the Sherman Act for entering into an agreements to distribute e-books through Amazon Kindles.
The lawsuit was filed by the Bookhouse of Stuyvesant Plaza, Fiction Addiction, and Posman Books at Grand Central.
Apart from Amazon, six publishers in the lawsuit include Random House, Penguin Group, Hachette, Simon & Schuster, HarperCollins, and Macmillan.
The plaintiffs claim that the use of digital rights management (DRM) for e-book sales is not fair to small book sellers.
The complaint alleged that Amazon has entered into confidential agreements with the Big Six publishers, who control about 60% of print book revenue in the country. This has since created a monopoly in the marketplace.
Alyson Decker of Blecher & Collins PC, who is serving as lead counsel for the bookstores, told the Huffington Post that DRM is a problem that affects many independent bookstores.
"We are seeking relief for independent brick-and-mortar bookstores so that they would be able to sell open-source and DRM-free books that could be used on the Kindle or other electronic ereaders," Decker said.
In May last year, Amazon reached a settlement with the Independent Publishers Group (IPG) over the sale of 5,000 e-book titles in the Kindle Store.