I think a big part of it is that JWs appear to be Christian on the surface and, especially in the US, being seen as attacking a Christian group is a big risk to take. Because of the large Christian population, Scientologists are seen as being obviously wrong in their beliefs. In essence, the Scientologists' bible was written recently and that makes it less mysterious and people are less inclined to see it as divine.
They also have more (and less insane) celebrities, and celebrities that are leaving and speaking out. It's a smaller group, which also makes criticising it less risky, but they have just as much public awareness as JWs so doing a piece on them is still worthwhile from a viewership standpoint.