In Skyrim, is it better to make a weapon or armour skill legendary if both are at 100?

Neither are good options^*.

Skyrim have scaling enemies and expect you to be at certain level of combat effectiveness. Dropping either of those skills to starting values will be highly detrimental.

To test it out, save before a fight that you don't have any problems with, then reload and make one of the skill legendary. You will find that the fight is now 10 times longer, or you are outright dead in seconds.

^*There is a caveat. If your Enchanting, Alchemy, and Smithing are all 100, and you are decked out in max enchanted gear with max boosted Smithing (even without the Restoration infinite Smithing bug), you'll still be invincible with all your skills at base levels.