Good day, it sounds to me like your looking to Subdivide the mesh, thereby "smoothing" out the peak to valley effect. This can be done with a Modifier as seen in this Three.js example:
http://threejs.org/examples/#webgl_geometry_subdivision
Now the basic principles here are:
1) use the latest revision of Three.js
2) pull down the SubdivisionModifier.js file and link it in:
<script src="js/modifiers/SubdivisionModifier.js"></script>
3) create the modifier during initializaion (play with the value, I tried 3):
var modifier = new THREE.SubdivisionModifier( 3 );
4) then after your vertices manipulation and before adding your geometry to a mesh to render apply the modifier like so:
geometry.mergeVertices();
geometry.computeCentroids();
geometry.computeFaceNormals();
geometry.computeVertexNormals();
modifier.modify( geometry );
Give that a try and let us know how it's working out, I'd be super keen to find out myself.