Developers and urban planning specialists have countered that New York has been a city in constant churn and that remaking neighborhoods is crucial to the city’s economic vitality and its place as a global capital.

On the Lower East Side, however, neighborhood groups say that Two Bridges will displace residents and raise property taxes beyond what people can afford. Francisca Benítez, who had spoken out against the development, said on Friday that she worried that the judge’s ruling was only a temporary setback.

“By refusing to approve these towers outright, the court disagrees with Mayor de Blasio’s total disregard for the community and his support for rich developers,” Ms. Benítez said. “This process is sure to get the towers approved with crumbs offered by the developers.”

Two Bridges would tower over Chinatown to the north and the Vladeck public housing project to the east. Thirty-seven percent of the residents in the surrounding area live in poverty — more than double the overall rate in Manhattan, according to the census. The median family income is about $27,000.

The striking income inequality throughout the city has spurred Mayor Bill de Blasio to pledge to preserve or construct 300,000 affordable units for poor, low-income and working-class tenants by 2026.

While the city is on track to have 200,000 units within three years, the mayor’s goal requires the cooperation of developers like those at Two Bridges. The developers agreed to set aside roughly 700 apartments in the buildings at below-market rates, which could make them eligible for generous New York City tax breaks.

It is not clear whether nearby residents could afford one of the units. About 300 of the apartments would be available to people who make about 40 percent of the city’s median income, which is about $43,000 for a family of four.