Officials arrested Mr. Fischer “without incident” after intercepting his 56-foot boat, known as The Silver Lining, at about 11:20 a.m. on Thursday as he was sailing on the East River toward the Long Island Sound, the Marshals Service said.

The vessel was registered under the alias Richard Graydon, according to the Marshals Service.

“This arrest demonstrates that time does not erase accountability,” Wing Chau, the U.S. marshal for the District of Rhode Island, said in a statement. “For more than 20 years, Ronald Fischer believed he had successfully escaped justice. The men and women of the Rhode Island Violent Fugitive Task Force, together with our partners, remained committed to ensuring that day would eventually come.”

On Friday, Mr. Fischer appeared at a hearing in front of Judge Jeffrey Gershuny in Manhattan Criminal Court. Handcuffed and wearing a light-blue polo shirt with gray khaki pants, Mr. Fischer agreed to waive his right to a formal extradition hearing, paving the way for his transfer to Rhode Island by July 31. He will remain in custody in New York until then.

George DeLuca-Farrugia, a prosecutor with the Manhattan district attorney’s office, said that the authorities had searched Mr. Fischer’s residence and found several books on “how to evade law enforcement.” Investigators also determined that Mr. Fischer had sent emails to his neighbors asking if the police were looking for him, Mr. DeLuca-Farrugia said. (Prosecutors did not say during the hearing where Mr. Fischer lived, and a spokesperson for the district attorney’s office declined to specify.)

Shanti Narra, a lawyer for Mr. Fischer, did not speak at the hearing.

After Mr. Fischer is extradited to Rhode Island, the state attorney general’s office will seek a sentencing hearing on Mr. Fischer’s rape conviction as well as an arraignment on a bail-jumping charge, Timothy Rondeau, a spokesman for the office, said.