Mr. Merritt of Ryder said he expected that some items that have already been advertised for sales on the day after Thanksgiving — traditionally the busiest shopping day of the year — would not get to stores in time.
The delays are hitting smaller merchants like Robert Van Sickle particularly hard.
His pet supply company, Polka Dog Bakery, was relying on a shipment of cardboard tubes from China with a merry design, intended to hold popular holiday dog treats. The products represent about 15 percent of sales at the company. But the New York Container Terminal in Staten Island, where the tubes arrived shortly before the storm, was devastated, and Mr. Van Sickle's freight forwarder has been unable to track down the containers.
It is too late to reorder the tubes from China in time for the holidays, and Mr. Van Sickle has tens of thousands of baked dog treats piled up at his Boston headquarters. Insurance will cover the cost of the cardboard tubes, but not the finished products, and those payments will not come close to making up for lost revenue.
Last week, he was forced to call customers like L.L. Bean nd tell them he probably could not fulfill their orders. "Without this product, we're in trouble," Mr. Van Sickle said. "I am a business owner and this is pretty much my year."
In Cape May, N.J., Rich Layton's six-week-old start-up, Layton Sports Cards, was supposed to be shipping sports card orders all week. But his apartment partially flooded, his Allentown distributor could not find clear roads to get to him, and U.P.S. held his other deliveries during the storm.
"It's thousands of dollars worth of cards that people were already paying for," Mr. Layton said.
As the days passed, Mr. Layton spent $1,000 on cards at a local shop, and gave most of them away on a live webcam feed to try to pacify customers. "It pushed my entire business back five days, and I've been begging and pleading with my customers to please be understanding," he said. He ordered replacement cards on Friday, paying $170 for overnight delivery so he could start distributing them to customers.
Wayfair.com, an online home-goods retailer, said about 1,300 of its 4,000 suppliers were hit by everything from loss of power to flooding. Niraj Shah, Wayfair's chief executive, said his site adjusted, removing two-day shipping offers for affected products and taking some merchandise off the site.
For suppliers who cannot get up and running soon, Mr. Shah said, "at this point, it is too late to get more inventory in for the holidays. If inventory's gotten ruined because of flooding or they're closed for two weeks, to be honest, it's a tough time of year for that."
Retailers are facing smaller headaches, too. At REI, whose SoHo store lost power last Monday night, employees took groups of customers around in the dark last week, aided by headlamps and flashlights. While the store was able to accept payments, its regular flow of merchandise was thrown off. Once power was restored on Friday, employees had to manually count and order merchandise, said Les Hatton, northeast retail director for REI.
Grocery stores and others that depend on perishable items are facing trouble, as delays of several days in meat or produce deliveries can mean ruined products. "They get impacted by the ability to access the stores because the roads are not repaired yet, the traffic, the ability to get even a truck driver to drive to the stores," said Kumar Venkataraman, a partner at the consulting firm A.T. Kearney.
As for Mr. Van Sickle of Polka Dog Bakery, he has been struggling with a sense of guilt for worrying about his dog food containers at a time when the storm has destroyed homes and killed people. He is considering repackaging the biscuits and donating proceeds to storm relief efforts.
"It's been really difficult to take stock of what's happening on the ground in New York and New Jersey," he said, "versus what's happening in my little office in Boston, where I'm calling my important customers and saying, 'I'm sorry, guys, I don't think you're going to get any product'."