Network.Instantiate players at each spawnpoint? Don't use the same spawnpoint?

For a prototype we did some time ago (with Unity 2.6) i simply checked the spawnpoints with Physics.OverlapSphere. Just make sure your spawnpoints are not too close. Usually your players are on a seperate layer, so you can pass a layermask to OverlapSphere to only search for players. Just iterate over all spawnpoints, check which ones are "free", put them in a list and randomly pick one from the list.

Example:

 // C#
 Transform FindSpawnPoint()
 {
     Transform[] spawnpoints = GameObject.FindGameObjectsWithTag("spawnpoint");
     List<Transform> freeSpawnPoints = new List<Transform>();
     foreach(var T in spawnpoints)
     {
         var players = Physics.OverlapSphere(T.position, 2, 1 << PLAYER_LAYER);
         if (players == null || players.Length == 0)
             freeSpawnPoints.Add(T);
     }
     if (freeSpawnPoints.Count == 0 )
          return null; // no free spawnpoints!!!
     else
     {
         return freeSpawnPoints[Random.Range(0, freeSpawnPoints.Count)];
     }
 }