even though i do not have indigos i did go through the process several years ago in anticipation of acquiring hatchlings. you will need to contact the NYSDEC division of endangered species in Albany NY. tell them what you are planning on doing and they will send you an application to fill out. i believe there was a $25 fee. if you are getting your snakes from a breeder outside of NY they may delay your state permit until you have your federal interstate transport permit.
the application asks a number of questions about planned captive environment and purpose for acquiring the endangered species. if you state that you are getting indigos for a pet they will not grant you a permit- this may be where they get the reputation for being difficult. you may have to come up with a plan for captive studies or educational purposes.
i hope this helps, best of luck.
dave b

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