What goes best with Shinobi? I've been trying to find a good ranged unit to go along with them, but I haven't been able to find a satisfactory combination.

Ninjas and albows are pretty good. But Ninja/Giant is basically the best ovo late game composition.

I feel like ninja-albows would beat giant-albows; wouldn't the ninjas easily be able to counter the giants via hit and run cloaking?

Not if you have merics to sustain. Several giants will just chainstun ninjas.

2+ giants and ninjas start getting messed up. More giants and ninjas won't get away.