Story: 3 little people, One Female and 2 Male, comes to big world (regular world) on ship through a stream, and they moved to a house with two kids. those kids used to have a doll house and the little people starts living in that house. than kids found out that someone is living in the doll house and they discover the 3 little people. One evil guy try to get hold of those little people. this story sets in like early 1900’s or late 1800’s.
Only parts of your description apply to my guess … I read a book as a child called “The Dollhouse Murders,” and certain elements seem to fit. If there was a movie made, they may have changed aspects of the story. Maybe this could be it?
sounds like some version of The Borrowers, though I can’t be sure as I haven’t seen them all.
http://en.wikipedia.org/wiki/The_Borrowers#Adaptations
also sounds a bit like The Littles.
http://en.wikipedia.org/wiki/Here_Come_the_Littles
http://en.wikipedia.org/wiki/The_Littles_%28TV_series%29