There are quite a few Two-Spirit and LGBT organizations that serve the indigenous community spread out across Turtle Island, AKA North America.
I have a lot of respect for the NorthEast Two-Spirit Society because it was when they hosted the 25th International Two-Spirit Gathering last year in Wading River, New York, that I first made friends with this community of amazing, caring, and talented people.
NE2SS has compiled a fabulous Directory of Resources that includes books, films, and contact information for these organizations across the land.
I'm including the document here, but you can find a lot more information on their website. Make sure to check them out.