Moving quietly, in any fashion, is stealth, regardless of the form of movement, IMO.
Now, swimming in rough waters while trying to be quite, would require a STR (swim) check and arguably a STR (stealth) (or DEX?) check. Depending on the noise made by the rough waters, the STR (stealth) check might be with advantage.
Swimming a long distance could easily become a CON (swim) at some point. But swimming quickly wouldn't require a check, as you would simply be taking the Dash action to double your speed. Unfortunately, moving faster isn't in the mechanics of movement unless you have a feature like Cunning Action to allow you another Dash.
Swimming while encumbered would be a STR (swim) check, because although the CON part comes up in doing it for a length of time, it is STR that determines if you can stay afloat or not IMO.
That is my take, anyway.