The accusations against David Waters and three others came in an affidavit filed in court by the Internal Revenue Service.
O'Hair, whose 1963 Supreme Court case led to the ban on organized prayer in public schools, vanished from San Antonio in 1995 with her son, granddaughter, and $500,000 in gold coins.
Authorities said Waters, who is jailed in Austin on weapons charges, allegedly orchestrated the plot to steal at least $600,000 from O'Hair's United Secularists of America.
But he also hated O'Hair, authorities said, fantasizing about "seeing Madalyn suffer."
The document names Waters; Gary Karr; Danny Fry, who was killed shortly after the O'Hairs vanished; and Gerald Lee Osborne.