I also highly recommend kakimori, which builds custom notebooks that you can select all the parts for (binding, paper, cover, etc.). Really memorable experience, and it's in a quieter residential part of the city (but still fairly convenient/central) that feels very different from the usual tourist spots.
Tokyu Hands was acquired by a major DIY store.
don't worry, Business will continue.
I'm hoping they can bring them back, though, there's nothing to compare to. In the meantime, online shipping works fine for what they happen to offer on the website, and that stock has increased recently, which is encouraging.
I can recommend their luggage in particular, there's just nothing quite like it.