Welcome to YT!!
Yes
all puppies from pet stores come from puppy mills/unethical breeders.
Do not purchase a puppy from a pet store.
Please check out this thread. It will help you find out which breeders are good and bad.
http://www.yorkietalk.com/forums/yor...e-breeder.html
I understand you don't want to spend thousands on a dog. We all have budgets.

However don't let price be your only determining factor. Find a very reputable breeder who breeds quality dogs that are sound healthy babies. You might have to pay more
upfront but in the long run your cost will be less as you won't have vet bills racking up in comparison to the potential vet bills of a pet store puppy. A cheap puppy could wind up being a very expensive puppy.
You can check out the YTCA breeder contact page:
Yorkshire Terrier Club of America About The Club
Take your time. Do your research.
Best of Luck!!