I can't read the writers' minds or anything, but just judging from game design principles, I'm pretty sure the relative rarity of those two examples specifically has nothing whatsoever to do with the balance of their features or convenience. Neither one requires attunement, both let you breathe water indefinitely as a standard action, one also gives you a swim speed while the other makes you swim normally. That difference is practically trivial.
One is clearly better than the other, yes, but from a standpoint of what they do in the game, they both accomplish the exact same thing: They let PCs explore places that would otherwise be cut off to them. For the game designer, and for the GM, that one feature is vastly more significant than the swim speed. So what if one is strictly better than the other? It's the GM who decides what you get, anyway, or that's the default assumption. (Arguably, this means the two are redundant and one probably shouldn't exist. Sure. Also arguably, the difference exists so that the GM can decide whether they want to give their PCs the slightly more down to earth or "gritty" cap that only lets you breathe or the flashier and more convenient cloak. Matter of preference here, though it also serves the function of pointing out that there's not just one way to do a given thing and GMs can make up their own magic items even if there's already something similar in the DMG.)
Actually, if we realize that the two do the same thing, we can also figure out why they're specifically uncommon, and not rare or common or very rare or legendary. If you look on page 135 of the DMG, it recommends certain guidelines for access to magic items, and says that uncommon items are appropriate starting at level 1 while rare ones are better for level 5 and up. Now, Water Breathing is a third-level spell, so that your wizard will have access to it starting at level 5, if needed. So after 5th level, giving a cap of water breathing or cloak of the manta ray as treasure is less significant, because if the PCs really want to get past some water, they probably have access to a way to do that anyway. So levels 1-4 are when these items are both at their most interesting and exciting (but they're not common because that would say things about the game world you don't want to say about every D&D game world).