Itachis crows can genjutsu, but the closest thing to hurting the puppies the crows could achieve is pecking the puppies eyes out. Thus the puppies win due to actually having the power to kill.
Pein's summons can actually attack, whereas the most Itachi's crows can do is cast Sharingan genjutsu (namely paralysing genjutsu). I'm unconvinced by genjutsu being all that easy to perform on a Rin'negan summon due to the shared eyes, though admittedly that's just a hunch. Even then, paralysis without the ability to attack is of no use.
Rin'negan puppies FTW. The crows can't attack, as others have said, so it'll be resigned to genjutsu which may or may not be effective on it. Plus, the dogs rapidly multiply which would make them even moreso difficult to kill.