Ultimately, it's your sister's decision, they're her children. In my opinion, the best thing you can do is answer the children's questions honestly and thoughtfully, but only if they ask you. Don't risk their parents cutting you off, and keep your mouth shut if that's what it takes. It's more important to have your sister's children in your life than to make sure they're raised the way in the way you think they should.
I'm not anti-Christian. I'm anti-stupid.