They were in cities and were generally in poor areas--The North did not use legal segregation laws but loophole laws allowed for whites and blacks to be segregated in the North.
The most popular reason why segregation in the North existed was suburbs. Suburbs were built by private contractors and therefore they could choose who to sell their homes to. Many made rules that the family had to be white and therefore blacks were not found in suburban areas. The process of redlining also kept blacks in less desirable neighborhoods unable to purchase homes due to unfair banking rules.