Etsy is pretty slick, although lately I've heard it has similar (but not the same) product/seller trust issues as Amazon.
iHerb has a somewhat Amazon-like UI but noticeably less cluttered and more structured. It highlights a minimum "best by" date, which is also a guarantee that goes beyond pure UI design but provides the kind of customer-friendly interface that informs rather than confuses.
I usually find Webstaurant product listings pretty informative and much cleaner.
From Big Tech, Google & Apple may not have a comparable physical goods marketplace but the marketplaces they do have - books and applications - are much cleaner and more focused than their Amazon counterparts.
Of course, the gold standard is McMaster-Carr.
I know Amazon is more successful than those examples. Microsoft Windows is also much more successful than its competitors, but I don't think most people would see that and argue "the point of an OS/software is not to be easy to use or convenient or understandable". Certainly it's not the point of Windows but I'd say that's because competition involves factors unrelated to quality and quality is multi-dimensional, not because quality is "not the point".