I must say Petco, only because its the only one out of the two thats near us.
They used to be HORRIBLE, but they've gotten a new manager, and its improved very much. No more bad bedding for the rodents (They use Carefresh now), No more dead fish in every other tank (though they still need to improve on the bettas), and its also the place where we met the humane society that Ethan was at.
The only pet I've ever bought from Petco was Ellison (my CT betta), and he seems just as healthy as my other bettas.
I do prefer the smaller petstores, such as the one in my town. It is a WONDERFUL place run by only around five people who take wonderful care of every animal there. And they actually know what they're doing.