What is the best way to make moving obstacles in a 3d game?

There are several ways to do this. I like having the obstacles on a navmesh and have them move to random locations upon entering their destination. You could put a randomizing script on the waypoints (below). first, you need a nav$$anonymous$$esh in the scene, then a nav$$anonymous$$eshAgent on the obstacles, then targets for them to navigate towards with the below script and a trigger collider. When they arrive at their target, they get instructions to go to another target. You need this script on the targets. This script is set up to randomize where the obstacles go. It is set up for 4 different targets. you would drag the other targets into the variable slot. OTHER targets! meaning target 1 would have targets 2,3, and 4. Target 2 would have targets 1,3,and 4. I tested it and it works. Tag the obstacle "obstacle". eventually turn off the meshrendereer for the waypoints so you don't see them

 using UnityEngine;
 using System.Collections;
 
 public class test$$anonymous$$ove : $$anonymous$$onoBehaviour {
     public float speed = 3;
     public GameObject[] targets;//possible waypoints for target to go to
     Nav$$anonymous$$eshAgent agent;
     public GameObject nextTarget = null;//actual waypoint the obstacle will go to. Leave this blank
     void Start () {
     
     }
         void OnTriggerEnter(Collider other) {
         if(other.CompareTag ("obstacle")){//your obstacle
             agent= other.gameObject.GetComponent<Nav$$anonymous$$eshAgent>();//gets the navmesh of the obstacle entering the waypoint
             nextTarget = targets [Random.Range (0, targets.Length)];//sets the next waypoint from the list
             agent.SetDestination(nextTarget.transform.position);//tells obstacle to go to tnextTarget
         }
     }
     void OnTriggerExit(Collider other) {
         if(other.CompareTag ("obstacle")){
             nextTarget=null;//resets the target for next obstacle when this obstacle leaves on his way to next waypoint
         }
     }
 }