Would the bulk of the taxes paid by Amazon be paid back? The article said that Amazon would get $3 billion in existing credits (i.e. not deal specific, just business tax credits) and would be paying ~$27 billion. Seems like a steal for NY.
If the basic premise here is that any company should get a tax break if they are capable of hiring enough workers whose tax payments would exceed their employer's tax payments, all you're doing is just shifting the tax burden onto the workers in the form of regressive income, sales, and property taxes.
You assume there is no economy of scale for government spending. For example, building a road to serve 10 million people may be cheaper per capita than a road for 1 million people. Same on the revenue side: doing a single large deal for $27B is probably cheaper than doing a thousand deals for $27M.
For there to be an actual increase in tax revenue for the state via income tax, those workers would have to be receiving higher salaries than they would have otherwise, would they not? Or emigrating from somewhere else, which they would be unlikely to do if they are not receiving an increase in compensation.
