hatsune miku merchandise
I guess the store with various goods would be Shin-Chitose Airport in Sapporo. Hatsune Miku is from Hokkaido and the Sapporo city tram is decorated with Hatsune Miku every winter.
Other than that, it seems like you have to search for multiple stores with small area dedicated for Hatsune Miku. Such as Animate, Gamers, K-BOOKS, Toranoana in Akihabara.