Until more information appears, the question of why the New York Independence Party chose no presidential nominee for the first time will go unanswered. The New York State Board of Elections had announced that ballot-qualified parties must choose their presidential nominees by September 10. Nevertheless, the New York Independence Party state committee went ahead with a meeting on September 22, and on the agenda for that meeting was the choice of a presidential nominee.
At the Albany meeting, State Chair Frank McKay proposed a resolution that the party not nominate any candidate for President, and that resolution passed. Nothing was said at the meeting, apparently, that at that point it was too late to choose a nominee. See this somewhat more detailed description of the meeting by Michael Drucker, a long-time officer in that party.