How many? How long have they been in our solar system (I'm asking so I can gauge the power levels of the Kryptonians)? Other than Superman and Majestic (the most well known of each race) are all the known members of the races included as well or are they just generic Kryptonians/Kherans?
Anyway, I'd say Kryptonians if the numbers of both sides are great and they're all on Superman's level. The biggest reason is because most Kherans/Kherubim aren't as powerful or as smart as Mr. Majestic. Most of them don't even have the same power set since the Pantheon (Majestic's class of Kheran) is one of 7 classes and the other 6 are very different. Only one of the others can even fly and none of the others has as much speed. They have some things like weapons that can kill Majestic level beings and psychic abilities, but those alone won't do too much if their best weapons (the Pantheon) are vastly outnumbered. If the numbers aren't that great then the Kherans might pull out a win, relying on their most capable Pantheon and Coda warriors to handle the bulk of the Kryptonians (aided by their specially forged blades and armor), the Titans and Spartan units for defending the psychics while they attack mentally, and the fact that almost every Kheran is a highly trained and skilled soldier bred for battle.