MJ and Ned attended the Massachusetts Institute of Technology, commonly called MIT, before the events of Spider-Man: Brand New Day. They later move back to New York after graduating.
Their education is part of the film’s new status quo. Both characters have continued their lives despite forgetting Peter Parker, while Peter remains nearby as an anonymous superhero. Their return to New York leads to Peter encountering them again.
Empire State University is a separate institution in the film: Bruce Banner teaches quantum mechanics there. That distinction can cause confusion because both universities are associated with major characters. MIT is the school connected to MJ and Ned, while Empire State University is connected to Banner.