I have looked into this a zillion times, it is legal to keep indigos in NY with a permit.If you are looking to get the endangered/threatened permit for keeping eastern indigos in New York, the gentleman to speak with at NYSDEC (at least as of Fall 2006) would be Mr. Joseph Therrien. His email is:
jetherri@gw.dec.state.ny.us
He can email or snail mail the application to you, I do not remember if there is any one time fee/annual fee involved with the permit.
One of these days I will get an indigo. In the mean time, good luck to you!
Dave Boyle