You ask for multiple perspectives: so let me start the ball rolling.

"Who are the top contemporary atheists working in philosophy today?" Maybe it's because I'm working in England which is a pretty irreligious country, but most of the good philosophers I know well enough to have any clue about their religious views are cheerful atheists for whom religion just doesn't feature in their lives (except when dingbat religious fundamentalists of one stripe or another cause public mayhem). And most of these philosophers aren't very interested in religion as a philosophical issue (they might casually wonder what it is about us which makes our minds prone to gripped by supernatural stories of one kind or another, but they don't think the supposed philosophical arguments for taking such stories to be true are worth wasting much time over). So most of the "top atheists working in philosophy today" round my neck of the woods aren't working in the philosophy of religion but are getting on with what they think is the serious stuff.

Occasionally, public-spirited atheistic philosophers will have a bash at spelling out the arguments. John Mackie's The Miracle of Theism is a modern classic (the miracle is that anyone is a theist, given the weight of considerations against). Robin LePoidevin wrote a good introductory book Arguing for Atheism a few years ago. In 2008, Louise Antony (a panelist here) edited a quite terrific collection of essays Philosophers without Gods: Meditations on Atheism and the Secular Life (if, from an English perspective, I have a slight complaint about that book, it's only that it overdoes the seriousness -- there's not enough mockery of the sheerly ludicrous aspects of religions). And then of course there's Dan Dennett's wonderful Breaking the Spell.

So the philosophical atheists haven't been entirely silent. But it does seem that much philosophy of religion is being written noisily by people with religious axes to grind (such indeed as William Lane Craig). When I've dipped into that stuff, I've thought it either badly argued or starting from premisses we haven't much reason to believe or both: so my impression is that, if the world of Christian philosophy has been "utterly transformed" of late, it is largely a matter of quantity rather than quality. But I am, like most of my colleagues, too unimpressed/too lazy/short of time to bother to really get to grips with it.*

*Though I did a couple of years ago bash away at length on my blog at a recent intro to the philosophy of religion by Murray and Rea: backtrack through http://www.logicmatters.net/category/religion/