If someone says science can't explain everything what's the best way to repond?

[Ben Davis]

That said, the methods of natural science... cannot make inquiry into the nature of being as such or the nature of causality.

Bold for emphasis: I think you'll find that's exactly what they were created for.

Natural science uses logic but doesn't explain why reason is effective.

Yes it does, every time a scientific model matches demonstrable reality. It shows us why reason is effective not only on a meta scale but specifically in relation to each scientific model. For any given model, predictions must be made with full explanations as to why those predictions will generate their outcome. When both the result and the reasons match with demonstrable reality, the model is considered robust and a theory is born. The 'why' is a critical and inescapable element of Theory and the religious position that 'why' is some sort of transcendent, ethereal, elusive component of existence is nothing more than a tool used to separate people from their reasoning so that absurd propositions can be inserted in its stead.

And it cannot speak to intentionality, meaning, or purpose. In cases such as these, the idea that science cannot explain everything is simply another way of saying that someone is relying on the wrong means to inquire about something.

Now this statement has more merit although saying that science has no input to this is just wrong. By making observations of the world around us, taking actions and examining their results, making predictions and holding our experiences against them, improving and refining our actions to generate results more in accordance with our desires, learning from the actions and inactions of others, we can gain much personal knowledge of intentionality and psychologists, sociologists & anthropologists can gain insight to models through meta studies. Much the same is true of meaning and purpose. Once again, these are not external things foisted upon us will he, nil he and religious insistence upon this fallacy is telling; religion fears reason.