I used both, I ended up settling on searxng because Whoogle seemed to be unable to retain my settings. Might be something with my cookie configuration, but searxng has no problem remembering my preferences. If that is not a problem for you then they are comparable; Whoogle is pretty simple to get going and works well, searxng is slightly more complicated to set up (but not that much with docker) but has a ton more features.

I looked into SearX but didn’t need all the extra features it has