You'll even find extremely knowledgable American history professors who use the term to describe Native Americans. Their graduate students, however, will tell you separately that they want and expect you to use more politically correct terms instead. Just has to do with the times.
In theory the rule is that you're supposed to refer to people by what name they prefer (e.g. "Little people").
Here's what Wikipedia says:
* The terms used to refer to Native Americans have been controversial. According to a 1995 U.S. Census Bureau set of home interviews, most of the respondents with an expressed preference refer to themselves as "American Indians" or simply "Indians"; this term has been adopted by major newspapers and some academic groups
A late-'90s Russell Means polemic against "Native American" (along with the fact that it got quite a bit of agreement) has been somewhat influential in that respect: http://www.nemasys.com/ghostwolf/Native/wai.shtml
So what is the problem with "indians" - is that word from a time when people thought they had discovered the passage to India?
Maybe just "natives" would be sufficient? Not all uncontacted tribes are in the Americas afaik (for example I've heard about a tribe in some Russian mountains).