The 40 AP one looks better as it can net you better items overall. I haven't bothered to run any of the others more than twice (2 times cause they were glitched and not giving out bonus reward which was fixed later but required you to run again) so I'm not sure if the 30 AP one can give you more than 3 ores but the 40 AP one gives 3-5 ores and the SSR EXP shield is obviously better than the SR EXP armor.

I've run enough to have gotten 3 Artemis Bows from the missions and have another mission which requires 100 ores. I've only managed to find 1 extra bow as a drop in the process. (So I have 4 right now.)