I can recommend you to read the book "Raising Freethinkers - A practical guide for parenting beyond belief."
It has a lot of good ideas how to strengthen the children's critical thinking skills.
I think you can only succeed if you with a lot of love teach them how to think critically for themselves. Don't talk negatively about the faith of your wife as it will be counterproductive.
Show them that it is normal that people have different feelings about religion or believe different things. The importance is not in what you believe but how you act.
They will see that you have a different belief than your mum. They will ask questions. Tell them how you feel about this or that bit never in a downgrading way.
I am father of a 3.5 year old boy who is heavily indoctrinated by his jw mum. Lately he said "in a church are bad people."
I try my best in counteracting this indoctrination and teach him critical thinking but also tolerance and respect for different views.
I will make it clear for him, that he can change his religion a thousand times in his life; I will always love him and be there for him.
I wish you all the best. It is not easy.