Firstly, if there is a full moon, the Saiyans will win with medium difficulties. And also, they have ki, not chakra, so Genjutsu won't have any effect.
Now, considering that there isn't a moon, I think that the Saiyans might win, with high or very high difficulties. Kaguya has Regenerationn, immortality and some space-time hax, and she haves 360┬░ vision, enabling her to dodge their attacks (Since, stat-wise, they seem to be on equal terms). Also, her Expansive Truth-Seeking Balls will prove to be a pain in the ass of the Saiyan duo.
However, we are talking about people who trained for combat since they were very young, born in a planet with 10X the usual gravity and that conquering planets is something that is pretty much common.
While Kaguya would be able to kill Raditz without that much of a problem, Nappa is very similiar to her in tier, and with Raditz' help, they can certainly hold her off on their own.
Now, Regenerationn will help a lot if she gets overpowered (Something that will happen). Until they start firing their strongest ki attacks, that will simply obliterate her, or at least, make a halt on her Regenerationn by hitting her multiple times with obliterating attacks. But that isn't going to be easy. One slight error there, and the saiyans will die by the Truth-Seeking Balls or will be badly trucked by the space-time hax.
Still, my money's on the Sayians.