The report by the Civil Rights Project at the University of California at Los Angeles looks at enrollment trends from 1989 to 2010.
In New York City, the largest school system in the US with 1.1 million pupils, the study notes that many of the charter schools created over the last dozen years are among the least diverse of all, with less than 1 percent white enrollment at 73 percent of charter schools.
He and his fellow researchers say segregation has the effect of concentrating black and Latino students in schools with high ratios of poor students compared with the statewide average.
Black and Latino students who attend schools that are integrated by race and income level perform significantly better than their peers in segregated schools, the authors note.
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The study suggests that New York's segregation is largely due to housing patterns but that it could be mitigated through policies intended to promote diversity.
Other states with highly segregated schools include Illinois, Michigan and California, according to the Civil Rights Project.
In New York, about half of the state's public school students were from low-income families in 2010, the report says, but the typical black or Latino student attended a school where close to 70 percent of classmates were low-income.
The typical white student went to a school where just 30 percent of classmates were low-income.
New York City Department of Education spokesman Devon Puglia did not address the findings of the report, but said, "We believe in diverse classrooms in which students interact and grow through personal relationships with those of different backgrounds."
New York State Education Department officials did not immediately comment.