He is being held on $5 million bail with his next court appearance Friday.
Meanwhile, federal prosecutors for the Southern District of New York also weighed in with additional hate crime charges against Thomas, a 37-year-old black man.
FBI investigators said they found journal entries allegedly written by Thomas in which he expressed antisemitic views, referencing Adolf Hitler and “Nazi culture.”
They said another journal entry allegedly stated that “Hebrew Israelites” had victimized “ebonoid Israelites,” which the FBI took to mean black Americans claiming descent from the ancient tribes of Israel.
Earlier this month, two armed suspects shot dead three people at a Jewish supermarket in Jersey City. The two assailants were killed by police.
The NYPD is currently investigating at least six different antisemitic attacks since December 13.
The UPI contributed to this report.