I would probably say movie Superman would be the favored to win, but he would have a rough go at putting Thor down. And if Thor is channeling lightening than he could rattle Superman.
That said, in the context of the JLA movie itself Superman was overpowered compared to the plot. The JLA were not needed other than Superman. Seemed like he mostly could have dealt with everything alone.
I was a bit surprised about how much stronger he seemed than Wonder Woman.
to make it a decent team movie...IMO JLA Superman was significantly stronger than he was shown in Batman v Superman, at least in how he was presented alongside WW and Batman's toys.
Based on BM v Superman and MOS, I might favor Thor...based on JLA, I'd probably swing slightly in the other direction, though as you noted, Thor seems able to take an absurd amount of damage.