Official police documents allege the two men used Twitter messages to contact protesters at the summit "and to inform the protesters and groups of the movements and actions of law enforcement".
In all, almost 200 protesters were arrested during the two-day summit, which brought world leaders to Pittsburgh to discuss the global economic meltdown and other matters of common financial interest.
About 5,000 protesters were estimated to have taken part in demonstrations in the city.
Twitter has rapidly established itself as an important tool in the armoury of protest groups and demonstrators. During the summit, the police openly monitored Twitter to listen in to the protesters' communications.
The FBI said that as well as the computers and radio scanning equipment discovered at the motel, they also confiscated from Madison's home 11 gas masks, five pairs of goggles and test tubes and beakers. They said they also took away anarchist books and pictures of Marx and Lenin.
Madison is a social worker with a Manhattan-based programme attached to a psychiatric hospital. He is said to be a member of the People's Law Collective, a voluntary group that advises protesters on legal issues arising from actions. Wallschlaeger produces a talk show on radio called This Week in Radical History.