I want to Randomly create an array of Thunder Sounds to play when the GameObject comes into scene.

In other words, I have a Random Lightning script that works perfectly to summon a Lightning.Prefab into the scene, this prefab also play a single audio with it, but I want it to play a random array of thunder sounds instead.

I am sure we would need to put this on the the Lightning Randomizer Script, so here it is:

#pragma strict
//Objects
var Lightning : GameObject;
var Box : GameObject;

//Box Attributes
private var BoxLength : float;
private var BoxWidth : float;
private var BoxHeight : float;

//random Values
private var randX : float;
private var randZ : float;
private var randY : float = BoxHeight;

//timer settings
private var timer : float = 0.0;
var Mult : int = 0.1; 

function Update () {
//seting up boundrys
BoxLength = Box.gameObject.transform.localScale.x;
BoxWidth = Box.gameObject.transform.localScale.z;
BoxHeight = Box.gameObject.transform.localScale.y;

//setting up the random values
randX = Random.Range(0,BoxLength);
randZ = Random.Range(0,BoxWidth);

//bringing the lightning in and randomizing the x and z
timer -= Time.deltaTime*Mult;
	if(timer <= 0){
		Instantiate(Lightning);
		Lightning.transform.position.x = randX;
		Lightning.transform.position.z = randZ;
		timer = 1.0;	
	}
}

Look at this. 2 audio sources on a game object, how use script to instruct one to play? - Unity Answers

Simply make an array of audio sources. Randomize between the array from 0 to length of array - 1.

Then play it, you should consider pausing when to play the audio or else you will get a lot of noises.