Manuel Hernandez, 46, wiped his eyes with his hand as he arrived for his initial appearance in Manhattan federal court on Monday.
He was not required to enter a plea and was released on bail.
Sara Sanchez and her five-month-old daughter, Antonella Garcia, died after the 22-foot Yamaha speedboat overturned late Saturday near the Statue of Liberty.
Twelve others were rescued and are in stable condition, authorities said.
The vessel was pulled from the water and taken to the New York Police Department's harbour unit facility on Randall's Island.
After state charges were lodged against Hernandez over the weekend, prosecutors said Monday that he will be tried in federal court, not state court.
Captain Doreen McCarthy, the Coast Guard Sector New York commander, credited the rescue of survivors to "heroic, swift actions" by those who responded from various agencies, along with a good Samaritan vessel.
Meanwhile, a GoFundMe campaign that began Sunday to help Andres Garcia pay for the funeral for his partner and daughter had topped $25,000 by Monday afternoon.
Antonio Russo, general manager at Il Punto Ristorante, said Garcia is an "amazing guy" who has been working long hours each week as a waiter, driver and food-runner, to provide for his family here and in Colombia.
Diego Naranjo, a neighbour of Sanchez in Queens, said he first met her last spring when her son threw a ball into their backyard. After recovering the ball, Naranjo invited her son to play on a trampoline with his children.
"They were really nice people. You can see when a person is noble," Naranjo said.
He said he last saw Sanchez last Tuesday as she brought groceries into her home. He said he was shocked by the deaths.
