I am pretty positive it's not Little Nemo.
All I can remember is a kid riding his bed in some sort of flood, and some other random weird stuff. I think there was a little creature that was the bad guy, someone got frozen in ice or maybe glass? And there was also a rainbowish tunnel that they traveled through?

Rock-A-Doodle Rock-A-Doodle (1991) (http://www.imdb.com/title/tt0102802/) was half animated, half live action and had a few scenes where characters were huddled on a bed while water was flodding higher and higher, it came out in 1991 and was exceptionally strange at points. I don't specifically remember people being frozen in glass or a rainbow tunnel though.