One cannot argue effectively against a religious worldview in isolation since religious believers will have other justifications for their beliefs, and explanations for why their views are not undermined by science. Thus, a complete attempt to refute a worldview must involve giving good reasons to replace these alternative sources with other sources and replace their views about meaning, morality and human life with non-religious views. Interestingly, there is at least one New Atheist who attempts to do this, and that is Owen Flanagan in his The Problem of the Soul.
It's nice to see someone actually mentioning Flanagan, who seems largely unknown outside of very narrow philosophical circles; and it would indeed be an improvement if more people read him. But I find the classification of Flanagan as a New Atheist odd. He's an atheist, of course, but that means nothing; there are atheists and atheists. Flanagan's 'quietist' atheism (to use his word) does not ever really sound like anything suggestive of anyone who typically gets designated with the label 'New Atheist', and he was recently, for instance, a signatory to the Neo-Humanist Statement of Secular Principles and Values, and Neo-Humanists are generally highly critical of New Atheists. Indeed, that was one of the reasons Paul Kurtz wrote the Neo-Humanist Statement in the first place. Now, Neo-Humanists are big-tent people, so there is a spectrum of views involved, and that means that there is a spectrum of possible sympathies with New Atheists. But even if Flanagan, the broadly Buddhist Neo-Humanist atheist interested in the possibility of a naturalized spirituality (or, as he has also called himself, "a Celtic-Catholic-quasi-Buddhist atheist"), has expressed explict sympathy for the New Atheism somewhere that I have not come across, it would not follow that he is best seen as a New Atheist. Flanagan is likely in a different camp altogether.
Flanagan provides a good example of why one should be careful with classifications when talking about anything so amorphous and different from person to person and group to group as atheism certainly is. This goes for critics and everyone else; it makes little sense to treat modern atheism as a monolithic position rather than as a cloud of many different droplets carried by currents in many different directions.