Possible Clues:

• Crossword editor Will Shortz's paper, for short
• Major paper, for short
• Paper read on the LIRR or Metro-North, perhaps
• WaPo alternative
• W.S.J. rival
• The Gray Lady of the press: Abbr
• Empire St. paper
• Big Apple paper, initially
• Big Apple daily: Abbr
• Pub. with more than 100 Pulitzers