Juan Thompson, 32, is set to appear in court next Monday morning to enter a guilty plea, according to the letter, submitted by Acting US Attorney Joon Kim in Manhattan.
Thompson's attorneys could not immediately be reached for comment. Before his extradition to New York, he denied the charges, said he had no anti-Semitic beliefs and said he was being framed and targeted as a black man.
"Make no mistake: this is a modern-day lynching," he said in a telephone interview from the Warren County jail in Missouri.
The prosecution's letter did not give details about the planned plea, which will not become final until Thompson enters it in court. Thompson was arrested in St. Louis, Missouri on March 3, and has been in custody since then, charged with one count of cyberstalking.
Federal prosecutors have said Thompson engaged in a vicious, months-long harassment campaign against his ex-girlfriend, using various email accounts to accuse her of possessing child pornography, driving drunk and, finally, making bomb threats targeting Jewish groups.
Thompson made some threats in his own name and then accused his ex-girlfriend of framing him, and made other threats posing as her, prosecutors said.
US authorities have been investigating a surge of threats against Jewish organizations, including more than 100 bomb threats against community centers in dozens of states in separate waves since January.
The organizations Thompson threatened included a Jewish museum in New York and the Anti-Defamation League, according to a criminal complaint in Manhattan federal court. All occurred after the first flood of phone threats in early January.Thompson was a reporter for the Intercept news website, which fired him last year saying he invented sources and quotes.