Possible Clues:

• NYC line
• N.Y.C.'s first subway co
• Lexington Ave. line
• Co. bought by NYC in 1940 that's found in the five longest answers
• Subway line to Columbia U
• Line to Wall Street, for short
• Subway whose first line had a terminus at NYC's City Hall
• Its first train ran from City Hall to 145th St
• Bygone operator of N.Y.C.'s Second Avenue El
• Subway line found in four of this puzzle's Across answers