
Yeah that one is good, one inherent problem... a submarine is subjected to a massive amount of stress, much more so than a boat/ship on the surface, this would also mean Noah would have had to totally water seal the wooden joints AND created an oxygen supplying mechanism AND a pressurization control method.
This would also have to apply to the window, was this window made of glass? in which case it would have to be water sealed too, if it was just a hole then the ship/boat would have pretty much had to stay just below the surface which is subjected to much more violence than being on top of the surface.
Also chances are a wooden submarine would warp and buckle so much it would be crushed under water.
Not to mention that wood is naturally buoyant and getting one to submerge would require a huge amount of ballast and require a power source to get it to the surface again. Ever tried holding a lump of wood under water?... wont stay there.
And to escape the violent turbulence of the surface it would have to go down a fair depth... sooo... yeah