Biogenic Upgrade is a card I’d recommend for hydras/counter-based creatures.

You don’t seem to run too much card draw — Greater Good is nice as it also helps fill the graveyard too.

Thank you for the suggestion, I love them both. I'm not sure how I forgot about Greater Good I took Crawling Sensation out for it, and for Biogenic Upgrade what do you think I should take out for it?

Needs more Vigor. You can resolve Vigor's replacement effect before resolving Polukranos's, so it gains counters instead of losing them. Does wonders for your other creatures as well. It will be a removal magnet, though. You could lean into the +1/+1 counter theme more with Oran-Rief, the Vastwood, Pir, Imaginative Rascal, Ivy Lane Denizen, and/or Renata, Called to the Hunt. Armorcraft Judge can provide more draw power, as can Rishkar's Expertise. Or you could go wide with Feed the Pack or Korozda Guildmage.

ghostofsparta thank you for these great suggestions :) , what do you think I should take out so I can fit those cards in?

I’d suggest taking out Nessian Hornbeetle, it’s a conditional, only on combat trigger, whereas the Ivy Lane/Renata add counters to all your creatures entering. You can take out a forest for the Oran-Rief land, and take out 1 forest and 1 swamp in exchange for Evolving Wilds and Terramorphic Expanse. Those will help get a couple extra cards into the graveyard and let you fix colours if really needed.

Unless you deal with a lot of burn damage, I would also replace Magebane Armor with Trailblazer's Boots to make Polykranos basically unblockable in EDH format.

Also, you could replace your least favorite hydra with Vigor. Play the deck a few times to see how those "enters the battlefield with counters equal to creatures in graveyards"-type creatures work out for you. I suspect that there will be times that your commander will eat their lunch, so to speak. Rhizome Lurcher seems to be the weakest of these, and this would be a good slot for any of the other cards I mentioned. Other cards to look at are Fungal Behemoth, Scute Mob, Obsessive Skinner, and Feral Hydra: if they're not pulling their weight when you test your deck then I would try replacing these with other cards.