As stated in other answers, the Natural Armor bonus is its own type. In terms of stacking bonuses, the general rule is that bonuses of the same type don't stack and only the highest is applied.
So if you have the bonus from the hedgehog familiar and you buy an Amulet of Natural Armor +1, the bonuses do not stack and you still only have a natural armor bonus of +1. If you buy an Amulet of Natural Armor +2, it will override the bonus from the familiar and you will now have a natural armor bonus of +2.
Other bonus types do stack, so casting Mage Armor will give you the +4 armor bonus on top of your +1 natural armor bonus from the familiar.