New York Deputy Mayor Alicia Glen sent a message Tuesday on CNBC to critics hoping to curtail $1.5 billion in tax incentives used to lure Amazon's so-called HQ2 to the city: "This deal is not going to get stopped."

When asked on "Squawk Box" about New York officials, such as Representative-elect Alexandria Ocasio-Cortez, who have come out against the move, Glen said the community would be engaged in the process.

"I can guarantee you five years from now all New Yorkers will be thanking us for having brought them," she said.

There has been some outrage buzzing from politicians who say residents of Long Island City, the Queens borough neighborhood where the internet giant is looking to plant new roots, would not benefit from the new development and that the tax breaks could be used to address other community issues. But Glen called the deal "job growth plays" that would generate $12.5 billion in tax revenues.

"A lot of that initial reluctance will burn off and people will realize what a great deal this is for New York City, because it's an endorsement of who we are as a city: innovative, diverse, open — and that's exactly why Amazon chose to come here to begin with," Glen said.

Glen, who heads up Mayor Bill de Blasio's housing and economic development department, explained that the online retailer is using New York's real estate and employee tax subsidy programs designed to "stimulate more job creation" outside of Manhattan.

Amazon could receive as much as $500 million in exemptions from the Industrial & Commercial Abatement Program and $3,000 per new job over 10 years from the Relocation and Employment Assistance Program, Glen said. If the tech company brings the 25,000 jobs it has promised, that could amount to $750 million.

Amazon was also offered incentives from New York state, which could sum up to $1.5 billion.

"This was not a deal that was designed for Amazon," Glen stressed. "These are our basic economic development tools and it again continues to diversify our economy into the five boroughs, which is actually the smart thing to do."

Worried that the new headquarters would jack up the price of living in the Queens neighborhood, Ocasio-Cortez is skeptical of Amazon's relocation.

Ocasio-Cortez has argued the plan doesn't correlate with the community's interests and would price out many working-class residents in the Queens neighborhood. The Democrat will represent parts of the borough in Congress when her term starts in January.

But Glen brushed off those concerns, promoting New York City's affordable housing program. The city is notorious for high rental and real estate costs.

"We have the largest affordable housing plan in the country, by miles," she said. "We have 300,000 units that are in the process of being preserved or constructed, and that's just on the affordable housing."

The Seattle-based company earlier this month chose New York City and Arlington, Virginia, as sites where it plans to invest a total of $5 billion and create 50,000 jobs. The Arlington project will reportedly get $573 million in subsidies.

Shares of Amazon are up more than 35 percent year to date.