Nicholas Rovinski, 24, was arrested yesterday. David Wright, 25, was arrested last week.
Both men are charged with conspiring with Usaama Rahim, 26, who was killed last week by terror investigators who had him under 24-hour surveillance.
Authorities say Rahim lunged at police with a military-style knife, but his family has questioned that account.
Rovinski and Wright, Rahim's nephew, were charged today with conspiracy to provide material support to the Islamic State group.
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The affidavit says the men initially planned to behead a political activist whom law enforcement officials have identified as blogger Pamela Geller.
Rovinski's lawyer, William Fick, declined to comment on the allegations. Rovinski is scheduled to make an initial appearance in US District Court this afternoon.
Wright's lawyer, Jessica Hedges, didn't immediately return a call seeking comment on the new charge. Wright has been in custody since his arrest last week on a charge of conspiracy to destroy evidence.
Two days later, Rahim called Wright and told him in a recorded conversation that he had "changed plans" and now wanted to attack "those boys in blue," referring to police, either that day or the following day, the affidavit states.
About two hours after that conversation, Rahim was approached in a parking lot by Boston police officers and FBI agents. Authorities say he was shot and killed after he pulled out a knife and refused commands to drop the weapon, the affidavit says.