Whirlpools are formed whenever two currents for a shear owning to differences in velocity. In a bathtub style whirlpool, the sheer is caused by the water accelerating down the hole faster than the surrounding water. This causes friction which is resolved by the generation of an ordered structure in the form of a whirlpool.
However, the most common whirlpools are those that occur in lateral flowing bodies of water. In many cases, they form under the surface so that are not observed in proportion to how common they are. When water is flowing around a bend, the water on the inside of the curve slows and the water near the outside accelerates. This will create a shear wall between the two that dissolve in to chaotic turbulences of lots of little whirls. The energy builds up the turbulence until the ordered whirlpool forms.
The whirlpool directs the water downward and by accelerating it creates a lubricating layer between the streams.
Such whirlpools can form and last for years. Some produce ice rings when the water on top freezes over.
To produce a sustain whirlpool that could suck down a ship. You would need either a single powerful current being bent along one side to create the shear or two current flowing suddenly adjacent.
In theory, you could get a whirlpool that forms like a tornado. Tornado's start when air get loft high by thermals cools and falls very fast downward and gets sucked but the thermal again. The forms a fast rotating cylinder of air with it's axis parallel to the ground. At some point, the cylinder goes vertical, concentrates and becomes a tornado. In theory, cold, dense high saline water crossing on top of warm, less dense water (optimally fresh) would sink rapidly, mix, warm and rise, drawing more cold into the system. If that cylinder turned on the side, you could have a sustained whirlpool.
In this case, you likely wouldn't have as sustained whirlpool but a dangerous region where such whirlpools could form without warning. Kind of an aquatic tornado alley.
If you want to suck down a ship with a plausible mechanism, I suggest aerated water. Gas bubbles in water lower it's density and ships become no longer buoyant. It's happened with fairly large vessels around volcanos and gas from hydrate beds is suspected in a couple of others.