You could use a For loop to set the first item in the loop to true and everything else to false.

if(currentWeapon == 0){     
    for (int i; i < weapons.length; i++) {
       if (i == 0) {
         weapons[currentWeapon].SetActiveRecursively(true);
       } else {
         weapons[!=currentWeapon].SetActiveRecursively(false);
       }
    }
}
else if(currentWeapon == 1)
{
    weapons[currentWeapon].SetActiveRecursively(true);
}
else if(currentWeapon == 2)
{
    weapons[currentWeapon].SetActiveRecursively(true);
}

(Sorry. I don't know the JS syntax but you should get the general idea.)

Both of the answers would work - my question is which would execute faster? Or is the difference neglible?

var weapons : GameObject[];
var currentWeapon = 0;

function Update () {
currentWeapon  = Mathf.Clamp (currentWeapon , 0, weapons.length);
    if(Input.GetButtonDown("YButton")){
    currentWeapon += 1;
    }
selectWeapon(currentWeapon );
}

function selectWeapon(index : int){
for (var i=0;i<transform.childCount;i++){
// Activate the selected weapon
    if (i== index)
       transform.GetChild(i).gameObject.SetActiveRecursively(true);
// Deactivate all other weapons
    else
       transform.GetChild(i).gameObject.SetActiveRecursively(false);
    }
}