It depends on which one is the original source. If a story has multiple versions, I generally prefer the original over the adaptation. I feel like it's a way of respecting the original author and experiencing the work as it was originally intended.
And I don't mean this only in the context of anime or manga. I feel the same way with adaptations from other mediums too. No matter how good an adaptation is, it can never convey 100% of the original creator's ideas, intentions, atmosphere, or nuances.
This is especially true for literature. There are plenty of light novels that have manga adaptations, and while the manga version can be much easier and more enjoyable to read, I often feel like something is missing emotionally. The original novel can spend more time inside the characters' thoughts, describe subtle emotions and atmosphere in ways that visual adaptations simply can't fully reproduce.
So if the novel is the original, I'll choose the novel. If the manga is the original, I'll choose the manga. Basically, I'm an "original source first" kind of person.