Some people were again forced to leave their homes and public transport was affected.
Winds gusted at up to 60 mph (100 km/h) bringing down trees and power lines.
New Jersey state governor Chris Christie said: “I am waiting for the locusts and pestilence next.”
Power companies in the two states report more than 100,000 customers suffered power outages. Some 650,000 buildings were already without power one week after storm Sandy struck, killing more than 100 people.
But the damage from the latest storm, a northeaster, was less than had been feared.
New York Mayor Michael Bloomberg said low-lying areas had not been flooded at high tide on Wednesday afternoon.
But Michael Bloomberg said he was still concerned about the security of those areas where flood defences had not yet been repaired.
He had closed parks and beaches and temporarily halted outdoor construction.
But he said there was no need for mandatory evacuations because the storm was not expected to be as strong as hurricane Sandy.
Long Island resident Rudi Schlachter, who was forced to move her family to the upper floors of their home due to severe flooding last week, said she was evacuating the area altogether now.
“All you need is a gale of wind driving a piece of wood into somebody’s window,” she said.
“We’re leaving; I don’t want my kids to see the water again.”
President Barack Obama spoke to the governor of New York and New Jersey on Wednesday, with the discussions focused on the continuing fuel shortages in the region.
Major airlines cancelled flights in and out of New York and New Jersey ahead of the storm.
So far 95,000 people have registered for emergency housing assistance in New York and New Jersey after Hurricane Sandy, according to the US Federal Emergency Management Agency (FEMA). It added that it was ready to deploy additional resources if needed.
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