I honestly can't tell you which is better as I've never even set foot inside a PetCo (for reasons I won't go into here) and I've only ever experienced one PetSmart program, with my Pomeranian. The main question is, do you want a well trained dog or do you just want to do a little socialization? Either way, you'll need to be careful if you choose a store option. I'll share my experience.
It's kind of a crapshoot as far as the trainers at these stores themselves go, you could be lucky and find a really good professional, or you could end up with some young newbie who only took the store's own training classes. You'd have to ask around at the stores near you I suppose to find out.
Anyway, I took my Pomeranian to the puppy class when he was almost a year old, the main idea was socialization (too late, I know, but after I got him we had a family crisis) and quite frankly the training in that class was ridiculously easy with stuff I'd expect most experienced dog owners to know already. I actually volunteered as a high level dog trainer at my local animal shelter for a few years, so obviously it was nothing new - I just wanted him to be in a group setting, away from home. If you're new completely to even teaching a dog to sit, it may be worthwhile for you to learn how. I don't know how advanced the other classes are as I only participated in the puppy one. Bottom line: There are better ways to socialize your dog for free.
As Rerun above me mentioned, you can't always count on the OTHER classmates to be ideal companions for your dog. In my particular class, there were THREE totally inexperienced new dog owners with large, older (8+ mos) pups that were extremely unruly, loud and obnoxious. Beau would growl and snap at them if they came near, because they approached him in the absolute wrong way, and no one would correct their animals properly when this happened. I got so sick of hearing these stupid owners cooing to them in baby voices, "awww be nice!" when they should have been correcting. When we did the walking bits around the store, those dogs pulled and dragged their owners around, and it never got better - a sign our trainer didn't really know all that much about any of it.
I would NEVER go to another one of those store classes, as a result. I found an actual obedience school nearby I will take Remi to when his shots are done. That way I will get better, quality advice and will be around dog owners at least committed enough to also take their pups to the right place. Plus it's got agility classes and other stuff, so once I find what Rem likes to do, we're already there to start!
Sorry if I went on long - but yeah, I don't recommend PetSmart.