Engineers have been ordered to find out within 30 days how torrential rain and heavy winds all but paralysed New York's transport system.
Commuters faced huge delays when floods hit subways and overground train lines during Wednesday morning's rush hour.
New York state Governor Eliot Spitzer ordered an assessment of the system's drainage after the third major failure of the system in seven months.
One woman was reported killed in a storm-related car accident.
New York city Mayor Michael Bloomberg said the woman died when her car became stuck in an underpass on Staten Island and was hit by another vehicle.
The mayor described how buildings had been damaged by rain in parts of Brooklyn - including a roof ripped off a church.
"I don't know that God had rush hour in mind when the storms hit," he said.
Some areas of New York experienced more than 3in (7.6cm) of rain in three hours on Wednesday morning, causing havoc on the transport system.
Many workers stayed at home as transport officials told commuters to avoid the morning rush hour.
Every subway line going into the central Manhattan area was subject to delays during the rush hour. Rail routes to the city from neighbouring New Jersey were also affected.
Flights from John F Kennedy airport were delayed by up to an hour and a half, and from LaGuardia by about an hour.
Metropolitan Transit Authority engineers were asked to report back to Mr Spitzer within 30 days with suggestions about how to deal with the chronic flooding.
The governor said there had been a "system failure", adding that there was a "design issue" that needed to be scrutinised.
There were fears of tornadoes as heavy winds damaged cars
Trees were uprooted during the storms, smashing into cars and blocking streets. Roofs were torn off houses and power cuts reported.
Elsewhere in the US, heavy downpours caused havoc - with parts of Nebraska being drenched by four inches (10cm) of rain in just one hour.
And more flood warnings were issued on Wednesday in northern Illinois, where flooding a day earlier had forced dozens to evacuate their homes.