Maybe Jack's weapon should be disabled underwater. Its not meant to be an amphibious unit as far as I'm aware.
Outside of that, locusts and gnats work pretty well as a quick reaction force against nonsense like that.
Also, big econ buildings/super weapons are worth placing some defenses around them in specific. If you put 2 faradays around a singularity, that's significantly improved protection for just 1/8 the extra cost. And if you put the singularity in a corner or side of the map, 2 faradays can cover all angles of approach.
I haven't tried this, but against flying jacks in specific, putting newtons around everything important may work well.
I find that is a good general rule about defense against deep raids: don't try to wall off your base, put the defenses directly around the important stuff. This way the enemy cannot avoid it.