It looks like you have taste since you mentioned Supergirl but let’s switch out Batman with Nightwing, yeah? Think about it like this… who can take down Batman better than his own apprentice? Bruce’s heart holds a soft spot for Dick that can be used to take him down! What do you think?
I say Harley Quinn would beat Supergirl because she beats Superman in Injustice. Also, if she has the green pills, there’s no way Supergirl would beat Harley Quinn.