UnityでMeshの頂点をムニャムニャする ref: http://qiita.com/divideby_zero/items/eef7604e306300fd7833

file2.cs

    private int cnt = 0;
    public void Update()
    {
        for (var i = 0; i < vertexList.Count; i += 2)
        {
            var v = vertexList[i];
            v.y = Mathf.Sin((i + cnt) / 20.0f);
            vertexList[i] = v;
        }
        cnt++;
        mesh.SetVertices(vertexList);
    }

MyMesh.cs

using System.Collections.Generic;
using UnityEngine;

public class MyMesh : MonoBehaviour
{
    [SerializeField]
    private MeshFilter meshFilter;

    private Mesh mesh;
    private List<Vector3> vertextList = new List<Vector3>();
    private List<Vector2> uvList = new List<Vector2>();
    private List<int> indexList = new List<int>();

    void Start ()
    {
        mesh = CreatePlaneMesh();
        meshFilter.mesh = mesh;
    }

    private Mesh CreatePlaneMesh()
    {
        var mesh = new Mesh();

        vertextList.Add(new Vector3(-1, -1, 0));//0番頂点
        vertextList.Add(new Vector3(1, -1, 0)); //1番頂点
        vertextList.Add(new Vector3(-1, 1, 0)); //2番頂点
        vertextList.Add(new Vector3(1, 1, 0));  //3番頂点

        uvList.Add(new Vector2(0, 0));
        uvList.Add(new Vector2(1, 0));
        uvList.Add(new Vector2(0, 1));
        uvList.Add(new Vector2(1, 1));

        indexList.AddRange(new []{0,2,1,1,2,3});//0-2-1の頂点で1三角形。 1-2-3の頂点で1三角形。

        mesh.SetVertices(vertextList);//meshに頂点群をセット
        mesh.SetUVs(0,uvList);//meshにテクスチャのuv座標をセット（今回は割愛)
        mesh.SetIndices(indexList.ToArray(),MeshTopology.Triangles, 0);//メッシュにどの頂点の順番で面を作るかセット
        return mesh;
    }
}

頂点をムニャムニャ

    void Update()
    {
        for (var i = 0; i < vertextList.Count; i++)
        {
            vertextList[i] += new Vector3(Random.Range(-0.1f,0.1f), Random.Range(-0.1f, 0.1f),0);//全頂点のxとyをランダムでちょっと動かす
        }
        mesh.SetVertices(vertextList);
    }