“It’s been very smooth,” Mr. Burke said on Wednesday. “Actually, today, I got there 10 minutes earlier than usual.”
Mr. Burke’s alternative route has become so popular with commuters that on Monday, the Long Island Rail Road added three Brooklyn-bound trains to Jamaica Station. During the morning peak, from 5 a.m. to 9:59 a.m., the number of commuters at Atlantic Terminal increased 50 percent, from 10,000 on an average day to 15,000 to 16,000.
Before the repairs began, Stacey Evans Greenberg, 34, used to take the Long Island Rail Road from Bellmore on Long Island to Penn Station, where she caught the E train north to her office near the Lexington Avenue-53rd Street stop.
She tried the Jamaica Station contingency plan twice, transferring there and riding the E straight to work. “Never again,” Ms. Greenberg said.
“My commute was over two hours,” she said.
The ferries were not a viable option for Ms. Greenberg, who lives in East Meadow. She said they were too far to drive to.
“I don’t think the contingency plan looked enough at where pockets of people live,” she said.
In New Jersey, the alternative bus routes and additional ferry service have been popular, said Charles Ingoglia, a spokesman for New Jersey Transit. Before the repairs began, about 3,950 commuters on the Morris and Essex Lines stopped at the Hoboken Terminal from 6 a.m. to 10 a.m. on an average morning. About 10,000 to 14,000 commuters stop there now during that time.
The PATH transit system, which has honored New Jersey Transit tickets at three stations — Hoboken, World Trade Center and 33rd Street — has also experienced an increase in ridership, said Scott Ladd, a PATH spokesman. The agency added trains on the Hoboken-33rd Street line during the morning and evening rush hours.
Patrick Smith, the spokesman for New York Waterway, argued that boats were the most reliable option for commuters.
“I can’t control when your train’s” going to get into Hoboken, Mr. Smith said. “But if you get into Hoboken, you know that every 15 minutes a ferry’s going to leave, and it’s going to take 12 minutes to get to 39th Street, where buses on five routes are waiting for you.”
Whit Waterbury, 64, is one of thousands of New Jersey residents who take the ferry to 39th Street.
“Traveling to New York City or from New York City on the Hudson River?” Mr. Waterbury said. “Nobody should complain about that.”
For Mr. Waterbury, the delays usually begin once he crosses the river.
“A couple of weeks ago, the E train was just dead, and my commute became two hours,” he said. “It’s usually 40 to 45 minutes. The 57th Street bus is a little better, but that adds another half an hour.”
Mary McCabe, 23, who lives in Manhattan, takes the 1 train to Penn Station because she works nearby. The commute has been a “nightmare,” she said.
“Trains are canceled, or delayed,” she said. “It’s been mayhem.”