I'm not sure I understand the question, Bombs are a supernatural ability.
I'm going to say the answer is "Both".
As far as rules are concerned both.
If a caster was in an anti-magic field the bombs could not be made inside it or thrown into it if they where outside the field.
There's a lot of fluff involved in bombs but they are for all purposes a standard action supernatural attack.
It's not like using a creation spell to make a bomb and you have an actual bomb that will set there forever.
A question recently came up to me about the Alchemist. While it's Bombs (Su) ability is listed as supernatural, there's been confusion as to which element is supernatural. Is it making the bomb that is supernatural, or are the bombs themselves supernatural? Or is it both?
Yes, bombs are magical. As I said in the other thread going on:
The bombs are infused with magic. They also don't function if handed to someone else. They are magic.
IF an ability is labeled as something (supernatural, extraordinary, or spell-like) then all of it is the same unless it specifically says otherwise. There may be a few abilities like that, but I don't know of any off hand.