i need to check which object (playing piece) the user has clicked on...but the problem is the else if block does not seem to detect the mouse input.

You are missing 4 closing braces } which should cause errors. If you just did not add them to your question then please add them to your question.

If I just add 3 closing braces } to the end of your script then this is what your code looks like

 void Update ()
 {
     if (chance == 1)
     {
         if (Input.GetKeyUp (KeyCode.Space))
         {
             if (enableInput == true)
             {
                 enableInput = false;
                 markers [0].gameObject.SetActive (true);
                 markers [1].gameObject.SetActive (false);
                 markers [2].gameObject.SetActive (false);
                 markers [3].gameObject.SetActive (false);
                 a.PlayOneShot (s_Dice);
                 DiceRoll ();
                 if (subPlayer == 4 && diceno == 6)
                 {
                     Vector3 temp;
                     Vector3 currentPos;
                     subPlayer -= 1;//3
                     temp = transform.position;
                     subplayers1 [0].transform.position = new Vector3 (startingpos1.transform.position.x, -1.8f, startingpos1.transform.position.z);
                     Invoke ("waitandgo",0.5f);
                 }
                 else if (Input.GetMouseButtonDown(0) && subPlayer == 3 && diceno == 6)
                 {
                     //print ("clicked");
                     //ray = Camera.main.ScreenPointToRay (Input.mousePosition);
                     //if (Physics.Raycast (ray, out hit))
                     {
                         print("Click");
                     }
                 }
             }
         }
     }
 }

But the code above will not see the mouse click. You are probably looking for something moe like this

 void Update ()
 {
     if (chance == 1)
     {
         if (Input.GetKeyUp (KeyCode.Space))
         {
             if (enableInput == true)
             {
                 enableInput = false;
                 markers [0].gameObject.SetActive (true);
                 markers [1].gameObject.SetActive (false);
                 markers [2].gameObject.SetActive (false);
                 markers [3].gameObject.SetActive (false);
                 a.PlayOneShot (s_Dice);
                 DiceRoll ();
                 if (subPlayer == 4 && diceno == 6)
                 {
                     Vector3 temp;
                     Vector3 currentPos;
                     subPlayer -= 1;//3
                     temp = transform.position;
                     subplayers1 [0].transform.position = new Vector3 (startingpos1.transform.position.x, -1.8f, startingpos1.transform.position.z);
                     Invoke ("waitandgo",0.5f);
                 }
             }
         }
         else if (Input.GetMouseButtonDown(0) && subPlayer == 3 && diceno == 6)
         {
             //print ("clicked");
             //ray = Camera.main.ScreenPointToRay (Input.mousePosition);
             //if (Physics.Raycast (ray, out hit))
             {
                 print("Click");
             }
         }
     }
 }