Here is a little comparison list, let me know if you have any other questions.
CityEngine Web Viewer:
* loads 3ws files (aka CityEngine Web Scene)
* displays a single static 3ws scene, exported from CE or ArcScene
* small local extent in cartesian coordinate system. (fishtank view)
* no authoring after publish (no basemaps, no adding of layers)
* initial one-time download, no streaming data.
Scene Viewer:
* loads web scenes
* displays a web scene created from Scene Viewer (AGOL) or Pro
* displays a collection of portal layers: Scene Layer, Feature Layer, Image Layer...
* World-extent in spherical globe rendering (or planar in local scene mode)
* World-extent basemaps
* loads data progressively
* Scene Viewer allows authoring of scenes, i.e. adding/removing layers, modifying symbology, create slides
* Use web scenes in WebApp Builder, Templates & 4.x JS API