I think the best way to do it would be with two variables:
Variable A is 'Focus/Normal Mode', and isn't actually a variable. Its value is always one, and it's activated by pressing the 'focus' button.
Variable B is 'Thermal/Alien Mode'. By default, it's set to 1, which is thermal mode. Pressing the button gives this authority over Variable A. Pressing it a second time alters to the variable to 2, changing it to Alien mode. Pressing the button when Variable 2 has both authority and is set to 2 turns the variable back to 1.
This way, the game would remember which vision mode you used last. Since there's a separate button to enter normal/focus mode, which cancels the special vision modes, the first press of the vision-changing button would go back to the last special vision mode you used.
I'm fairly sure this is how they'll do it, seeing as though there's a separate button for focus mode and from what we've seen, focus mode cancels the special vision modes.