A view of the waterfront of Long Island City in the Queens borough of New York, along the East River, on November 7, 2018.

New York City's deputy mayor for housing and economic development, Alicia Glen, told CNBC on Friday, her last day in office, that she'd like to see more women running big companies — and if that were the case, deals like the now-scuttled Amazon headquarters plans for Queens might have different outcomes.

"Maybe if there weren't all these men running companies we would possibly have different results," said Glen, whose office spearheaded the Amazon HQ2 deal that fell apart last month, in the face of local protests led by liberal politicians such as freshman firebrand Rep. Alexandria Ocasio-Cortez.

"If there were more women running large companies, there would be a different way in which people engage with communities. There would be a different way in which people started to threaten to leave, etc.," Glen said in a "Squawk Box" interview. When asked whether that stance could be seen as sexist, she said, "I don't think it's sexist at all."

Last month, New York State Sen. Michael Gianaris defended his opposition to Amazon's HQ2 proposal for the Queens neighborhood of Long Island City. Queens is one of the five boroughs of New York City. The others are Manhattan, Brooklyn, The Bronx and Staten Island. "Amazon needs to get ahold of what they mean to communities, and act responsibility," he told CNBC at the time.

However, many other New York politicians and CEOs are trying to get Amazon founder and CEO Jeff Bezos to change his mind. They wrote an open letter, which appeared in The New York Times, saying a "clear the majority of New Yorkers support this project." The effort, paid for by the Partnership for New York business group, said Democratic New York Gov. Andrew Cuomo "will take personal responsibility for the project's state approval," and Democratic New York City Mayor Bill de Blasio "will work together with the governor to manage the community development process."

William Ford, chief executive of New York-based growth equity firm General Atlantic, told CNBC's "Squawk Alley" on Friday that the city's letter to Amazon does not seem needy. Ford, one of the signatories, said the message to Bezos is, "We want you to reconsider."

Glen, whose departure was announced in December, told CNBC that the city remains committed to the original Amazon deal, which included city and state performance-based incentives of about $3 billion. Those perks were at the heart the deal's opposition. However, Glen said the incentives offered by the city are available to any company that wants to bring operations to Long Island City.

"That is where the mischaracterization and misinformation about the basic deal continues to be in the ether," Glen contended. But she did acknowledge that the state's incentives were specific to Amazon.