I actually have had a lot of trouble with greninja in general. Not just when using Pac-Man. From playing some really intense games with Pac v Frog, I've found a few handy things though.
A lot of Greninja's "WHAT DO I DO" inducing game is just throwing water shurikens and following them up with grab/ Dash Attack mixup. This in and of itself is kind of a ***** because of how many things in this game are relatively low commitment, and our grab is on the slow side. What I found worked really well was the hydrant. When he throws water shurikens you can set it in between you two while grabbing a projectile, start wailing on it to fling it at them, or stand on top of it and mess with em with your water shenanigans.
Hydrant in general seemed to do work in this matchup. When they start to use counter too often you can just drop a hydrant and do the Side B thing (it needs a name). They try (read: fail) to counter the hydrant, it's a freaking hydrant so you know how well that works out, then they got bopped by you and or the hydrant.
Greninja also tends to combo very vertically, and we all know how well Uair does against ****ing HYDRANT
Hydrant in this MU works for me, but it could just be personal experience against people who don't know how to deal, so keep that in mind.
Edit: I also just figured out a filthy edgeguard. Like, seriously amazing how much **** is going on.
Basically, you set the hydrant right on the side most part of the stage, Z drop a green fruit on it, and do literally anything after that. The green thing throws the hydrant stopping them from ledge hopping/ ledge jumping, as they have to deal with avoiding both hydrant and green. They can't Nair to grab the green because hydrant will break their face. They can't attack from ledge because green bounces off hydrant and will bounce off them if they get up attack. Same with just ledge get up. The only thing it doesn't cover is staying on ledge and ledge roll, which you can guess/ read and use a move to cover.
One of my favorite parts is that when the green hits the hydrant and bounces, it will bounce again when it hits the opponent, so if you do a choice DA or Nair you can grab the green and set the whole fun house up again.