I'm not sure you could say much about the difference in puppies, if one is registered or one isn't. I think its really important to find a breeder you believe in, and find out how much they know about the breed, and if they've done important health screening on the dam and sire. When choosing a puppy, price is probably the least important factor, if you get too good of a bargain, it may be because the breeder skipped some important and costly tests. You have to decide what's important to you, Yorkies can live 16 years, and will be an important part of your family, choosing a breeder that is actually trying to improve the breed means choosing a breeder who breeds to standard, which is 7 pounds and under. It also means silky hair instead of cotton, which is 100 times easier to care for, and will save you many grooming hours. Adding a pet to your home should not be an impulse decision, it's one that takes time, much like adopting a child, I think. Here's a good link to finding a good breeder.
http://www.hsus.org/web-files/PDF/Good_breeder.pdf