I think the Zora Mask is the best over all water travel, because you're a Zora. It's fast, it's agile, and it lets you do much more than just swim. You can walk underwater, damage enemies while swimming with the electric shield and slash them while standing on the seabed, and you can jump out of the water onto platforms you couldn't otherwise reach or would take time to pull yourself up to. Though there are places they could improve it, so far nothing has been better than the Zora Mask, and I have doubts that anything will unless they bring it back or let you be a Zora some other way. The Zora Armor is the closest after this, but it feels very slow in comparison. However, I really like it that you can use items while swimming, like the clawshot, and using the sword underwater was a pleasant improvement from OoT. I wonder what the Mermaid Suit would be like in a 3D game...
And for the above water travel, the King of Red Lions is pretty good and goes fast, but constantly have to change wind direction got a bit annoying, so I'll say Demetri. He can swim up waterfalls.