Chewy.com has very good prices on most things and as long as you meet the free shipping minimum you'll be paying less than stores typically. I've also used Wag.com once or twice (for me their shipping is even faster). But my go to more recently has been Pet360.com. This company is also the parent of PetFoodDirect.com but Pet360 seems to offer better prices and terms. The prices are not necessarily better than Chewy but Pet360 has been big on coupons that save 15-20% additional.
In the end it pays to check several because which is cheaper can vary a little depending upon the specific items you are buying.
I use Chewy mostly but today place an order with Wag.com. I can get Nutro Natural choice less at Petsmart so I buy it there. You have to shop around. Overall I like Chewy the best.
I've used Chewy for awhile, until my friend told me about Ebates. Chewy unfortunately wasn't one of the online stores that they work with to give a certain percentage of money back, but Pet360 was! They give you 7% back, plus I find that Pet360 quite often has 20% off your order! If you miss one, you're sure to find another 20% off promo a couple days later! Sure, they don't offer as wide a selection as Chewy, but you can save a lot more money using Pet360!
I just made an order from there and got about $14 back from making a $200 order of food and cat litter using the Ebates thing, PLUS 20% off, bringing it down to around $160. So I saved about $55! Sounds good to me.
I'm not sure if anyone here has heard of Ebates, but it's a great way to earn some money if you do online shopping.