from a fluid dynamics perspective, ...i.e. control volume w/ mass flows in/out, ..the velocity and flowrate, all other things the same, is all that matters... ever see that new jet suit, that sucks up water from the surface and pumps it up to a jetpack on the guys back thrusting him upward? could extenuating things alter the velocity and flowrate - sure, ...if for instance the difference in the pressure on the exhaust side (which is why boat engines can produce more power by dumping their exhaust above water rather than below, i.e. "through-hull exhaust)...
The problem is you are not making the dual comparison of air/water release.
How fast would that "jet pack" be going if instead of floating in the air, he were to remain submerged under water? If he were to stay under water, he would accelerate much faster due to the resistance of the water that is surrounding him.
I never said that the water coming out of the squirter would not accelerate ANY, I simply stated that the actual propulsion value would be greater if released below the water line than above, as the OP was asking.