Wait until you are sure, then tell them together I think.
My hand was forced after DS (4.5) and I found exP and OW together in our home. ExP left shortly after that, after some shouting so DS knew there was something up.
We both sat down with him about a week later and explained that Daddy would not be living with us anymore, but that he'd still see him loads, could call him whenever he wanted etc. We were as honest as we could be but I've avoided blaming exP (although it's all his fault) and just said that sometimes Mummies and Daddies don't live together. Initially I said that we had a fight and that we are not friends anymore but I've avoided saying that since as I don't want DS to think that if we have arguments, one of us will leave. I also want him to see exP and I having a civil relationship (which we are managing even though I want to cut exP's genitals off with a rusty spoon...)
I was talking to a friend who's parents split up when she was 5 and she said the worst thing was not knowing what was going on so we've tried to be as honest with DS as we can about what's happening and give him specifics i.e. Daddy will pick you up from nursery but when Mummy gets home, Daddy goes and Mummy does bedtime.
How old are your children? They probably know that something is up. I found a good book in the libary called "Mum and Dad glue" that is suitable for smaller children, which emphasises things being different rather than bad, which is the line we've tried to take with DS.