Hi there! I've gotten several ponies signed before, and from what I've heard, you're going to want something that's called 'archival ink' - it's acid-free and designed to last a long time. The brand I use are called Micron, and they've seemed to hold up very well so far! The ponies I got signed with Sharpie have, unfortunately, faded even over the brief time I've had them. (I didn't pre-seal them, however, so that might prevent bleeding/fading!)
The only problem with Micron (not sure about other archival pens) is that they don't 'flow' as well as a Sharpie, so if your autographee is anticipating a smooth-flowing pen, they might be confused.