Tough call really.
BYB can be ok if the people have their hearts in the right place and some semblance of knowledge.
Puppy mills...I wish there was a way we could just do away with them.
Frustrating as all hell to deal with the puppy mill puppies we get at the clinic (most of the time). Then we get the rescues who take the mill puppies and adopt them out...which is another kettle of fish.
I was going to go with a breeder for our Spoo pup, one that I knew was probably a BYB, but I knew two dogs that came from her,and they are both nice, well behaved, smart dogs. And then I just happened to look on Petfinder(which I usually know better than to do!) and saw Flip with a rescue. We really have no clue what his story was, aside from that he was a 'breeder relinquish' in Alabama, and ended up with a local rescue here in Milwaukee. I am guessing he is back yard bred, but who knows? Until he can learn to talk, we're SOL
I am a firm believer in 'knowing' when you see the dog, if it is going to be a good fit for you. I trust my gut...and every time I haven't trusted it, I regretted it.
So, if you end up saving a dog from a puppy mill, a rescue or a BYB, be ready to deal with issues.
That isn't to say that an impeccibly bred dog won't have issues either, but probably less likely.
Do what is right for you and your family, is the moral of the story. Know what you are prepared to deal with.