Real estate is a finite resource. NYC isn't some dying rust belt town, someone will setup shop where Amazon planned to, and they will pay taxes that Amazon thought they shouldn't have to pay.

How is Amazon taking more than what they paid for? Think of a building with apartments for rent. Half the apartments are empty and the building is falling apart because the rent doesn't cover repairs. The building manager offers new renters 20% off for a year. The existing renters protest and the new renters back out. You don't suddenly end up with more money to cover repairs.

No one is saying that money is being produced out of thin air.

Think of it this way. Walmart doesn't pay some of their employees enough to survive, so those employees get food stamps. Walmart makes enough profits to pay those people the equivalent value in food stamps, but they don't. It can be said that the government is giving Walmart some amount of money because Walmart's profits are higher because of the food stamp expenditure.

The federal government is not sending money to Walmart via a bank transfer, but there is an exchange of money taking place.

Now think about this in terms of city services. Twenty five thousand employees would not pay enough taxes to make up for what they use in city services combined with what the organization uses. Certainly not 3 billion dollars worth. In that sense, the 3 billion dollars could be seen as NY basically paying Amazon to give 25K professional class people jobs. There are other social side effects that are hard to assign a dollar value to.

Does that make more sense? No one is saying that money would come from no where. It helps if you assume for a moment that your ideological opponents are actually smart people who aren't just deluded, but that they have an interest that is actually in opposition to "your side".