A top Al Qaeda operative plotted to smuggle weapons into New York Harbor in the shipping containers of a Garment District firm, the Daily News has learned. Days before he was captured in Pakistan in March, suspected 9/11 mastermind Khalid Shaikh Mohammed met in Karachi with the owner of a W. 35th St. clothing importing company and his son, law enforcement sources said. Al Qaeda's No. 3 man offered to invest $200,000 in International Management Group in exchange, federal authorities now believe, for access to IMG's Port Newark-bound shipping containers, sources say. Mohammed "is obsessed with attacking the United States,...