Hi Wendy No difference. Both of the other words should be hyphenated - non-native and non-indigenous, although you could use other words, such as 'alien' or 'foreign', depending on context.

I agree,there's no difference.Perhaps the distinction between these two words is that "native"pertains to origin of birth in one place eg. i am a native of Davao,Philippines. On the other hand,the word "indigenous"is commonly used to describe a social standing of the people.Those who are needy;destitute of means of comfortable subsistence in life.