I think Thor would be much faster than Spider-Man, going by those feats. Spider-Man doesn't even have real super-speed like an actual speedster, just a bit better than "peak human". It's not like he can catch speeding bullets. One thing I noticed (and which no one else seems to have) is that Thor dug that trench before Quicksilver could escape. While Quicksilver is a lot weaker than the Flash, he's still faster than a speeding bullet, I believe (mach 5, IIRC?), so we can say that Thor definitely has serious speed. How big was that space of land across? A couple hundred feet? How long would it take someone moving at several times the speed of sound to cross that distance from one end to the other?
As for Thor having trouble with Mongoose and that alien karate-fu lady, that's just some shabby writing, I would say.