Why is it that you don't like to support chain stores? For most people feel that way, it is due to things like labor practices, standard of care (in the case of pet store chains), monopolies or business practices harm communities, or just the idea of the giant faceless corporation out-competing Mom and Pop (I.e, scale).
Not coincidentally, those are all the exact reasons why chain stores are often cheaper than the small locally-owned competition.
Standing on principle is all well and good, but sometimes it means paying more for things, and that's still true whether you can afford to or not. If you can't afford to follow your principles with your cash, that's the way it is. But don't try to stand on principle about how you want pasture raised beef, handmade bread, and organic vegetables - and then expect people to sell it to you for the price of a big Mac.
At a certain point, you have to accept that Petco can afford to price match for feeders and the locally owned place can't or won't. Either your principle of not liking chain stores is worth paying the price difference, or it isn't. That's still true of you have limited funds.