Both have the same concept an old videogame that secretly holds a living entity in it. But the Godzilla Creepypasta never explained to us what it was making it scarier, Ben just some slightly crazy kid trapped in a video game eh. In Godzilla the game is the monster in Ben a kid who we're told right off the bat is a ghost. Godzilla led up to Zenith which is crazy as ####. Ben didn't really build up to much except stick him on the Internet (yes fridge horror implications but really unless he shuts down the Internet then he's not really that scary). Now Godzilla isn't perfect my problem is that some of the sprites look funny (Solomon reminds of Squidward the way he moves and demeanor Best 1973!) which ruins the immersion some times.
In all fairness maybe I missed something or I wasn't in the mood and I also only read act 1. So maybe it gets better in later arcs? To Ben is like "The Shining" only without the climax and just builds up to nothing.
TL;DR: NES Godzilla Creepypasta > Ben Drowned.
"You shouldn't have done that,"