Due to the incredible relevance of the issue, I must share my opinion on ssb64 tiers. >.>
Link is better than Samus in the abstract because of his ability to control space with projectiles and actually combo pretty well, but I don't think he really has any good matchups. Samus at least has one decent matchup in Jiggs, just because neither of them combo each other and Samus' bair is huge and shuts Jiggs down.
Isai can do really well with link (as can other really good players) because they can play well enough to not really get hit, which is Link's main weakness (how few mistakes he can afford to make). Going by matchups and assuming equal skill, though, Samus is probably a little better.
So it depends on how you look at it. Most people would probably say Link > Samus. (Samus is so bad... ><)