I don't necessarily disagree with them, and if it was up to me, I'd rather Amazon land in Dallas that probably needs the jobs more.
However, this will be an objectively good thing for NYC as a center of commerce, and help establish it as a tech hub at a time its local job market isn't doing all too well.
Moreover, I doubt Amazon will game the system so excessively that it won't end up paying in taxes and investment and influx of business and salaries much more than it will receive in tax breaks.
It's unlikely they'll game the system so badly because it's not wise to screw the municipal authorities that can make your life miserable.