A boy gets kidnaped and raised by an indian tribe and his parents keep looking for him.they find him toward the end of the movie but the stays with the tribe I think john lithgow plays the father in that movie

The only movie I could find with John Lithgow, having to do with Indians, is:

At Play in the Fields of the Lord (1991) - IMDb (http://www.imdb.com/title/tt0101373/?ref_=nm_flmg_act_60)

I hope this helps, but I doubt it. The story isn't the same as what you posted.

If its possible that the Indian tribe you remember could actually be a tribe from the Amazon rain forest, then maayybbee this is what you're looking for (also - it stars Powers Boothe, who could maybe be mistaken for John Lithgow ( old memories are a funny thing... )) :
The Emerald Forest (1985) - IMDb (http://www.imdb.com/title/tt0089087/?ref_=ttpl_pl_tt)
...The American engineer Bill Markham moves with his wife Jean Markham and children to Amazonas to work in the construction of a dam. When he brings his son Tommy to the site forest, the boy is abducted by the tribe of the 'Invisible People' and brought to rain forest. Bill spends ten years seeking out Tommy in the forest. When he finally meets Tommy, he is an Indian and does not want to leave his tribe and return to the civilization....