I would tend to suggest another non-waterproofing solution - build something to hold your ship from underneath, that will safely rest on the bottom of your pool.
Of course, if you don't want it to show on the picture, you'll have to be extra careful about how you do it, but I think it's the simpliest solution.
What I would do is buy a large plexiglass sheet (or any other transparent material), make sure your ship is secured to it (drill some 8mm holes in the plexiglass and poke studs in them, or Technic Axles, or whatever). Then you can have someone hold the sheet & ship slightly under water so that the ship looks like it's floating, whereas it's actually not. As long as the borders of the sheet are outside of your camera frame, you're in business.
I owe that idea to a Stargate SG-1 episode I rewatched recently, actually. In the making of, they explaing how they make it look like a bullet is floating in mid-air - they just embed it in a plexiglass sheet and film right through it. It's it's good enough for commercial television, it should work for you too.