You might start with the 'His Dark Materials' trilogy by Philip Pullman. Pullman jokes that Harry Potter undeservedly gets all the flak from Christian groups while his trilogy was unapologetically about killing God and destroying the Church. It's subtle but it's there.
Salmon Rushdie, The Satanic Verses
James Morrow,Towing Jehovah
There is also Douglas Adams with his subtle jabs at religion in his Hitchhiker's Guide to the Galaxy books...
"In the beginning, the universe was created. This has made a lot of people very angry, and is generally considered to have been a bad move."
"He hoped and prayed that there wasn't an afterlife. Then he realized there was a contradiction involved here and merely hoped that there wasn't an afterlife."
“Your God person puts an apple tree in the middle of a garden and says, do what you like, guys, oh, but don't eat the apple. Surprise surprise, they eat it and he leaps out from behind a bush shouting "Gotcha". It wouldn't have made any difference if they hadn't eaten it.'
'Because if you're dealing with somebody who has the sort of mentality which likes leaving hats on the pavement with bricks under them you know perfectly well they won't give up. They'll get you in the end.”
“I refuse to prove that I exist says God, for proof denies faith, and without faith, I am nothing. Oh, says man, but the Babel Fish is a dead give-away, isn't it? It proves You exist, and so therefore You don't. Q.E.D. Oh, I hadn't thought of that, says God, who promptly vanishes in a puff of logic.”
Small Gods and Feet of Clay by Terry Pratchett...also The Last Continent