I think both manta ray bosses are equally common so other variables must determine auction price. I think manatarune's colour scheme is more appealing but wave sweepers seem to go for a higher price. Perhaps it is a balance of enough people wanting mantarunes and more people selling them which ends up making them cheaper, idk.
Maybe it has to do with their elemental alignment? I fight with a mostly plague team, which is weak to ice attacks. Mantarunes can wipe out one of my dragons in one hit, so I usually never finish fights with them. Plague is resistant to plague, though, so I can take on the sweepers with no issues, even if I'm just fighting with two 25s and a fodder. If enough users are fighting in the kelp beds with dragons weak to ice, then maybe it's affecting the numbers. I think one of the very popular guides recommended plague dragons before the new bosses, so maybe a lot of users are using them as their leveled teams?