It's generally up to personal preference, as the Isle of Armor is very easy and more focused on character development with Kubfu than actual battling. However, against the final battle against Mustard, Venusaur slightly edges out Blastoise, as it has the potential to hit more Pokemon for super effective damage -- particularly if you chose the Tower of Darkness for your Kubfu. The battle against Honey is irrelevant, as her party is different for both starters. Against Avery, Blastoise is generally the better pick, as it's not weak to his Psychic STAB. Against Klara, the choice is once again irrelevant.
Tl;dr it really doesn't matter. Determine whether your team needs a Grass or a Water type more, and choose based on that.