The judge's decision affects the state and city orders temporarily, until hearings are held for Apple Tours to defend itself properly.
Allowing the city and state orders to remain, however, would irreparably harm Apple Tours, she said.
Hayim Grant, the president of Apple Tours, would not comment yesterday.
Apple Tours has had problems almost since it began operations in 1992 with two used buses.
In its nine years of operation, Apple Tours has had hundreds of regulatory and safety violations.
Apple Tours started with two used buses before switching to its signature British double-deckers.
But he said his company would not accept tickets bought from other operators or directly from Apple Tours.
Apple Tours announced in February that it would close down after a fatal accident and citations for more than 1,000 violations.
Apple Tours challenged the order, saying it violated the company's rights to due process.
Some in neighborhoods where Apple Tours has racked up violations were unhappy.