Co-owners Ian Reisner and Mati Weiderpass, who also own a large stake in gay beach resort the Fire Island Pines, faced mounting criticism both online and from hotel clients after the meeting.
AIDS charity Broadway Cares canceled a May 10 event set to be held at the hotel's club, 42 West, because of the meeting, they said in a release.
"We cannot in good conscience hold an event at a venue whose owners have alienated our community," they said in a statement.
A Facebook campaign boycotting the pair's properties had garnered over 4,500 supporters by Friday, and called the meeting with Cruz "a devastating blow to the community."
But the hotelier pair says they were only trying to bend Cruz's ear on gay marriage, they said in a statement.
"I was given the opportunity to have a candid conversation with Senator Ted Cruz on why he should rethink his view on gay marriage," said hotel co-owner Ian Reisner.
"My support for Hillary Clinton remains steadfast and my meeting with Senator Cruz was a chance to engage head-on with Hillary's opposition."
Reisner and Mati Weiderpass said the pair agreed with Cruz on policy relating to Israel.
"We spent most of the time talking about national security issues and in particular the challenges regarding the defense of Israel to ISIS and Iran -- these are the only issues where we found common ground," Weiderpass said.
Representatives for Cruz did not immediately respond to requests for comment.