My favorites already listed, so I will mention David Cross and Patton Oswalt.
Penn Jillette is definitely a good one. Fair, but tells it like it is from his perspective. I like that. I also enjoy Lewis Black. George Carlin was one of the best and I go back for his stuff over and over. Then there's Doug Stanhope. Julia Sweeney is another good one, but not quite in the same league. John Cleese, Jim Jeffries, Ricky Gervais, and Stephen Fry are all great. There are just too many to limit it to just a few.
Tim Minchin's name should be mentioned here.
Just had this post-we need to research before posting. Bill Maher and George Carlin
Two of my favorites
I'm not sure John Cleese is by definition an atheist. He is very critical of religion, but I'm not certain that he calls himself an atheist, Eric Idle of MPFCs certainly is. He once said he believed in the doctrine of separation of church and... planet. My favourite atheist humourist is of all time is the late Dave Allen. In a class of his own.