Amtrak was stopping northbound service at New York City's Penn Station. Part of Amtrak's Downeaster service, which runs from Brunswick, Maine to Boston, was also stopped according to spokesman Cliff Cole.
Authorities suspended service on commuter trains into Boston as well as the city's subway called the T and the city's buses. That includes the Silver and Blue lines between Logan and downtown.
All major highways remained open, according to the Massachusetts Department of Transportation. The exception was in Watertown, Mass., the center of the manhunt.
Megabus canceled at least 22 buses between Boston and New York, New Haven, Conn., Hartford, Conn., Burlington, Vt. and Philadelphia. More than 1,000 passengers were affected, according to spokesman Mike Alvich. They received emails offering a refund or the option to rebook for free.
Bolt Bus, Greyhound and Peter Pan Bus Lines also suspended service. Passengers booked on canceled Bolt trips received refunds to their credit cards, according to Timothy Stokes, spokesman for Greyhound and Bolt Bus.
Across much of the Boston area, streets that would normally be bustling were quiet.
In Somerville, a densely populated city of about 75,000, authorities requested that residents stay inside with doors locked and not go to work.
People largely heeded officials' pleas, said Bob Trane, an elected alderman in Somerville, which abuts Cambridge, about 5 miles northeast of Watertown.
"I'm just like everybody else in Greater Boston, just staying at home, glued to the television," Trane said. "There is nobody out in the streets, very few cars, very few people walking."
Logan airport remained open, although getting there was a challenge for many passengers. On a typical day, the airport has about 1,000 flights. Fewer than 10 flights had been canceled by 10 a.m., mostly because of weather delays in New York, according to flight tracking site FlightAware.
The airport has been operating at a heightened level of security since Monday's attack, according to Matthew Brelis, director of media relations for MassPort, the public agency that runs Logan.
The Massachusetts State Police set up a roadblock Friday morning and were searching some of the vehicles entering the airport.
While no mass transit was reaching Logan, private cars, taxis and the Logan Express a bus service to suburban park-and-ride facilities were still able to enter the airport.
The biggest hassle for travelers were taxi lines, which Brelis described as "exceedingly long" during the late morning. Officials were asking people to share cabs to nearby location. By noon the backlog had cleared.
Friday's manhunt capped off a tiring and emotional week for Boston residents.
"This thing just doesn't stop. It's been constant for the past week," said Ian Deason, director of Boston operations for JetBlue, the largest airline in the city with about 120 daily flights.
He noted that pilots and flight attendants resting in a crew lounge prior to their flights were "glued to the TV" and the security presence at the airport was significant. But operations were normal for the airline, which allowed anybody scheduled to fly to or from Boston to change their ticket for free. Passengers could also opt to fly to Hartford, Providence or any of the New York area airports JetBlue serves.
Delta Air Lines which has about 70 daily Boston departures also hadn't canceled any flights. Spokesman Morgan Durrant said the airline expected on-time departures and was considering extending a travel waiver issued earlier in the week.
US Airways was running its 70 daily flights with minimal delays. The airline is letting passengers change tickets to any other flight through Monday.
American Airlines hadn't canceled any of its 31 daily flights in Boston. The airline was allowing passengers scheduled to fly today to rebook onto flights Saturday or Sunday without penalty, according to spokeswoman Andrea Huguely.
United Airlines has about 100 daily flights in Boston and allowed anybody flying Friday to rebook for anytime within a year of the day their ticket was purchased.
Southwest Airlines allowed passengers flying Friday to change their tickets to flights within the next two weeks. It's AirTran subsidiary is allowing changes to flights through Monday.
The Federal Aviation Administration imposed an air traffic restriction on the Boston area "to provide a safe environment for law enforcement activities." It barred flights below 3,000 feet in a radius of 3.5 miles around the manhunt area. The restrictions had minimal impact on commercial flights in the area.
James Kearney, an information technology consultant from East Amwell, N.J. was in town for business and managed to make it out on a United flight at 10 a.m. He said via email that the 15-mile trip from the Marriott in the western suburb of Newton to Logan on the Massachusetts Turnpike "was extremely quiet during rush hour."
Once at the airport, he said, the situation was "pretty standard."
"Even security was fast and uneventful," Kearney wrote.
Colin Alsheimer, who was on a flight from Dallas to Boston Friday morning, said that the manhunt dominated conversations during boarding.
"People were checking for news updates on their phones and talking with their seat neighbors," Alsheimer wrote in an email from the American Airlines flight.
After landing at 12:15 p.m., Alsheimer said the airport was surprisingly normal.
"People do seem focused on news broadcasts in terminal bars," he said. "Only saw an increased security presence on the road leading into Logan. Must be focusing more on departures."
Kacey Brister, a senior at Louisiana State University, was supposed to have an interview for a public relations job in Boston at 3 p.m. Friday. She was flying on Southwest Airlines from New Orleans to Boston via St. Louis.
Before boarding the last leg of her trip, Brister said that everyone was fairly calm at the gate.
"The biggest concern for most people was how they were going to get from Logan to their hotel, home," she wrote in an email, adding that there was "a sense of camaraderie between passengers."
Not everyone was so calm, however. "My mother has begged me" to turn around, she said.
Mark Jewell contributed from Somerville, Mass.