Complex sentence: The Second Avenue Elevated had one station at 86th Street and Second Avenue--right above the same intersection where the under-construction subway station is located--while the Third Avenue Elevated had two stops on nearby Third Avenue at 84th Street and 89th Street.
Split into simpler sentences: The Second Avenue Elevated had one station in the vicinity of the under-construction 86th Street station at 86th Street. The Third Avenue Elevated had two nearby stops on nearby Third Avenue at 84th Street and 89th Street.