there is really no such thing as "the best food". since every dog is different, but with the additional info you gave we can get a little closer to what you are looking for.
if you are limited to big chain stores, there isn't much good stuff out there. the only good food petsmart carries is the "blue buffalo" line. nutro natural choice ultra is not a bad food, but it is quite a step down from blue and much more expensive than even some of the really high end products.
petco is even more difficult, the only thing i'd buy from there is natural balance. i have seen that some individual petcos carry solid gold now, which is good (i'd rather buy that than nutro natural choice ultra), and on their website they sell eagle pack, and the holistic varieties of that are also good quality.
for the top-quality foods you'll have to go to smaller, independent pet stores (or small local chains/franchises) or feed stores.
all questions of individual needs aside, the best thing on the market (in my opinion) is currently innova evo. it's a completely grain free food that contains far more meat than anything else out there and has top-quality ingredients, no synthetic vitamins and is manufactured in a very gentle cooking process that preserves nutrients better.