Anyway, my wife and I have discussed how we're going to deal with this many times. Luckily, we've always been on the same page. Neither one of us is very interested in telling him what he should and should not believe, but at the same time, we aren't too interested in hiding how we feel about things. (My wife has recently started describing herself as an atheist as well.)
While dinking around on Facebook just a few moments ago, I saw an ad for an "atheist children's book". The main point of the book is that there are many religions out there, and that they're ALL not true! (Even Shintoism? Say it ain't so!) I was intrigued enough to check out the link, but I don't think that I'll be buying it. After all, I don't feel the need to have a book for my son that explains that Star Wars isn't real, do I?
Giving him a book like that feels a bit too much like doing one of the things that I don't like about religion in the first place - telling kids what to think, rather than simply teaching them how to think. In other words, it's indoctrination, and while a certain amount of indoctrination is valuable, I think it's best to avoid it when you can. (When is it valuable? When it comes to teaching him to treat people fairly, not steal, etc.)
Personally, I'd rather just share Bible stories with him along with stories from various religions around the world. I have a My Book of Bible Stories that I got for him (it was free, but I remember it from when I was a kid) and I'd be willing to get him other children's books based on The Bible or any other holy book. I'll read him those stories the same way I'd read to him the stories of Zeus and Odin out of the mythology books that I have for him. I won't feel the need to tell him at the end of those stories, "Ya know, Zeus ain't real, son." So why would I do that with the Jesus stories?
The big difference is that he'll no doubt run into people who believe in Jesus (and a few others). He'll probably ask me about it. I'll tell him that I don't believe it, and I'll tell him my reasons for not believing it. I feel confidant that I have good reasons for not believing those stories, and I feel that ultimately he'll be more swayed with my reasoning over their dogma. And if I'm not using reason, then he shouldn't be listening to me about that in the first place.
But let's be TOTALLY honest with ourselves though. For a good portion of his childhood, he's going to believe what his parents believe no matter how we present it to him. The trick is planting the seeds for critical thinking when he's young, so that way he can truly make up his own mind when he gets older.
I guess that atheist children's book would be of value for religious people to give to their children, just so their kids can see why nonbelievers don't believe. Fat chance of that happening though, I reckon.