Do you mean to defend not just atheism but logical positivism, of all things? Logical positivism has been demolished. It's antiquated and obsolete. Secular reason did the demolishing, the same kind of rational scrutiny that supports atheism.
My point in that first criticism is similar to Daniel Dennett's portrayal of the concept of natural selection as a universal acid; reason is just such an acid that even eats itself, leaving us in the state of "postmodern" hyperskepticism, malaise, and cynicism.
It's disingenuous for the atheist to castigate theists for being irrational, when secular reason has already eaten away at its foundations, both in philosophy and science. The pretense that atheism is ultimately rational is creaky, since it perished along with the Newtonian, mechanistic picture of nature.
I grant in that first criticism that "postmodernity" is wrongheaded if it entails that every statement is equally true or equally false. Science is indeed a superior way of understanding natural events. But the best epistemology these days is something like pragmatism, certainly not logical positivism. And pragmatism makes for a defense of theism, too.
Moreover, science's expertise in nature has little to do with any strength in handling ultimate questions about what may lie beyond or give rise to nature. If anything condemns theism once and for all, it's philosophy and aesthetics (good taste in fiction/myth), not science.
Just to be clear, I'm not saying these top three criticisms suffice to disprove atheism or that they're so overwhelming that they ought to compel everyone to be theists. I am an atheist. But atheists aren't all equally wise.