There are good and HORRIBLE examples of both.
It is easier to make decent AMVs because the source material can only be so bad, with fanfiction, the sky's the limit. However, there are some professional authors lurking around writing fanfic, and the quality and skill put behind a few very rare examples hasn't been matched by any AMV I've ever seen.
Not surprisingly, the best stuff has nothing to do with animu, it's all in the novel fandoms. You have to be reasonably literate to even become a fan, so it's not surprising that the best writers tend to write about books.