Going to japan

You forgot about Hokkaido

Obviously Akihabara, a lot of manga shops with yaoi and hentai, figures, arcades, etc.

https://www.japan-guide.com/e/e3003.html

I'd recommend checking out ikebukuro otome road there's a bunch of merch there aswell as any animate shops u come across (๑•ㅂ•)و✧

Harajuku is about fashion, not otaku, you won't find a lot of shops related to it. People dress up in more extreme fashion there.

Harajuku is not a single street or are you thinking about a particular street in Harajuku?