I think they are, yes, but the problem I have is that they often don't have a set appearance in the anime timeline. Their place in the story can be figured out to an extent based on what Pokemon the characters have and such, but no mention of movie events is made outside of the movies. The reason for this, I assume, is that in case one did not see the movies, one would still be able to follow what goes on in the show. A very obvious example of that would be when Ash meets Articuno in Johto and... whips out the PokeDex rather than just saying "Look, it's Articuno".
Um... that tangent aside... I think they are canon because they are made by the same people, set in the same regions that are being traveled in at the time of production, with the same characters who have the same Pokemon. It's really just a bit of a side quest to whatever they were doing before.