A strategic response
Some atheists insist that “Theism is ridiculous; God is a magical being, like Santa Claus. In this sense God resembles an invisible pink unicorn, or a flying spaghetti monster, and performs miracles, which are magical”1 This is a staple complaint from New Atheists in particular, and their figureheads.2 When you encounter it, try proceeding one of two ways:
1): Ignore it and focus on arguments. In the end, they are just wanting to (rudely) say that God is kooky from the perspective of their naturalistic worldview. Say:
“I think that maybe you're just communicating that theism seems ridiculous to you. But, if you can do that, then people can just as easily dismiss atheism or evolution when it seems ridiculous to them. I think it's prudent to set aside our feelings about what is ridiculous, and look at the actual arguments. Do you have one you'd like to go over? If not, I have a few for my position that I could present to you.”
1): Challenge them on their definition of magical.
Step 1: Ask them for their precise definition of magical (get it on the table).
Step 2: Offer your definition. Try saying something like:
“It seems to me that, in stories with magic, the magic is always supposed to be part of nature. Yeah, it's a weird part or hidden part of nature, but magic is still always represented as being part of nature. They are always law-governed in some way or another, which is why you have to chant or work the magic in specific locations, and often it is a commodity that you can run out of. God, by contrast, is supernatural, and so not subject to any natural laws. So, if there were magic in the world, God could eliminate it or entirely re-write all the magical laws.”
Step 3: Finish by offering them alternatives. For example,
“Maybe you just mean God is weird and non-scientific? Or perhaps you mean there is no mechanism behind God's actions and miracles.”
Unless your interlocutor is just wanting to be insulting, normally it is the oddity of God that is the fundamental issue for the naturalist; that is the challenge he is really wanting to raise, and that challenge has not been addressed simply by establishing that God is not technically magical. The non-believer needs a new way to represent his fundamental objection, or he will feel like nothing has actually been answered by your technical objection. In other words, he is liable to resist and continue defending his “God is magic” thesis just because that's how he is comfortable representing the issue. If you give him a good alternative (“you just mean God seems weird and non-scientific”), he is far more likely to feel comfortable giving up the technically erroneous “God is magic” line.
A more sophisticated possibility is that your interlocutor means that there is no mechanism that mediates God's interactions in the world, which seems to highlight the unscientific nature of miracles. But in fact, unmediated interactions are required on naturalism, and ultimately any worldview. Every naturalist needs to affirm the existence of fundamental entities (e.g. space, electrons), and these fundamental entities will have “basic powers.”3 The electron is thought to be an elementary particle with no substructure, and as a fundamental particle, it has its own set of fundamental powers that are not explicable in terms of other mechanisms. For example, it has an intrinsic angular momentum (spin) of a half-integer value, and there is no mechanism behind this; it just does it. If God exists, God similarly is a fundamental entity with fundamental powers (for example, the power to make free decisions for reasons).