If you've ever seen that "This is my hole" meme, the story Enigma of Amigata Fault is where that originated from. A personal favorite of mine is Long Dream. And a longer series of overarching stories called Uzumaki is great as well.

he has a bunch of shorter stories that you could easily jump into without any order but i'd recommend reading uzumaki first. its a classic, is one of his longer mangas, and encapsulates a lot of what makes ito's stories unsettling. i've never actually gotten one of the short story collections so i can't recommend any in particular, but i've yet to read an ito manga i regretted reading so i would say just pick whichever one interests you the most.

also, if you're into cosmic horror, i recommend hellstar remina since i don't see it talked about as often as his other stories.