Giving the incentives is the screw up. Not how they implement it. Even though they often implement stupid policies and ignore the things they actually need to pay for. In many cases, states and local governments lose hundreds of millions, if not billions, trying to attract investment which doesn't pay off.
Kansas City lost 331 million in tax revenue due to horrible policies that incentivized moving jobs a mile across a river to a different state. https://www.npr.org/sections/money/2016/05/04/476799218/epis... http://www.kansascity.com/news/local/article183014956.html (video embedded, pls 2 watch)
Kentucky gave tens of millions in tax breaks to build a Noah's Ark theme park. http://www.cnn.com/2016/07/07/us/noahs-ark-kentucky/index.ht...
New Jersey wants to give Amazon $7 Billion in tax breaks. It still has not invested money in fixing its broken public transit system. https://www.wsj.com/articles/newark-offers-7-billion-in-ince...
In other words, construct a hypothetical move for a hypothetical corporation to some example town, and I'm sure that town could come up with an incentive package that would be beneficial to its citizens in place of having the company not move there. Do you disagree?
I'm claiming your argument is suspicious because it seems to only really apply to organizations of Amazon's size. Maybe you disagree, but it sure doesn't seem like any cities or towns are interested in luring an Amazons worth of businesses and tax-payers that aren't a single organization. The argument seems pretty agnostic; why is no one else?
Moreover, there only seem to be three such zones in the entire state: parts of upper Manhattan, parts of the south of the Bronx, and some parts of Yonkers.
What money are they giving away? If Amazon never comes, then there is no Amazon taxes and thus no tax breaks.
Right now those towns are starting out at zero. If they are smart, they structure the incentives to make sure they are net positive. If they screw that up, well that's on them.