There were 2 children (brother and sister) who for some reason were on a boat on a choppy river (think) and they go through a rainbow and end up in a fantasy land

The Great Land of Small (http://www.imdb.com/title/tt0093116/?)?

Oh my God thank you so so much!! That has taken me years to try and figure that out. My sister and I can now rest at ease.

Glad to help.