Overall, 19 suspects were charged, and some appeared in federal court in Central Islip.
Some of the arrests were made at the House of Tattoos in Rocky Point, the club's Long Island headquarters.
Among those arrested were John Richard Ebeling, Jr., also known as "J.R.," who was the president of the Pagans Long Island chapter, and now oversees the activities of Pagan chapters on Long Island, Sullivan County, New Jersey and eastern Pennsylvania.
Also arrested was Jason "Roadblock" Blair, who succeeded Ebeling as president of the Long Island chapter in May.
Federal authorities say the Pagans were growing in strength as they plotted against their bitter rivals, the Hells Angels, who maintain a chapter in Hempstead.
The suspects were charged with conspiracy to murder members of the Hells Angels and the Hells Angels Associates.
They also were charged with assault, distribution of cocaine and oxycodone, conspiracy to commit extortion and weapons charges.
The arrests were part of a four-state operation that included 300 ATF agents, as well as state and local police.