Although the sake tide seems to be rising in Europe in general, there are still just a handful of places in Zurich. (Geneva has a larger Japanese population and a much better selection, so I often end up going there for specific things.)
If you know of any more places in Zurich that are good for sake please let me know!
Run by Yuko Suzuki and Markus Baumgartner, this little shop not far from the main station (Europaalle side) has a carefully curated selection of Japanese gifts (pottery, lacquerware, knives), food (rice, wasabi, miso), tea, spices/condiments, homemade miso and amazake, and sake. Their stock as of June 2018 includes Taka (Nagayama Honke), Kikusui, Tensei and Hojun (Kumazawa Shuzo), and Rojo-hana-ari and Hana Fubuki (Nishiyama Shuzo). They also give regular evening workshops on sake and fermented food (mostly in German but some in English). Sometimes closed when they go to Japan to visit suppliers, so check the site or sign up for their newsletter for advance warning.
Sato Slow Living
Also not far from the main station (Landesmuseum side, near the Museum für Gestaltung), Sato is part furniture/furnishings shop (if you need tatami matting or a real futon in Zurich, this is the place), part gift shop with a selection of crockery and washi paper. What amazed me when I first came across their online store is that they carry Onna-joshu, the sake brewed in the tiny village of Iwamura where I lived during my year on the JET programme! They also stock the Hyakushun range from the Kosaka brewery in Mino, and sake and skin care products made with sake lees from the Funasaka brewery in Takayama - all from Gifu Prefecture! My German wasn't good enough to get the whole story but it sounds like they have an arrangement with the local government in Gifu Prefecture. They also do occasional events, details on their site or in their newsletter.
As far as I know the only dedicated Japanese food shop in Zurich, their main shop is a little way out from the city centre (Guggachstrasse tram stop) but they have opened a new branch near Stadelhofen station. Their website shows a rather restricted selection of sake, but ignore that and go in to the Falkenstrasse shop where if you're lucky the young woman in charge of the sake selection will be there to show you more, and more interesting, bottles. Their range as of June 2018 includes Okunomatsu, Sawanotsuru, Mukai Shuzo, Yagi Shuzo, Hikami, Mikunihare, Honda Shuzo, Tsukasa Botan and Kubota. They also have amazake and Japanese cider. Nishi also runs the Bimi restaurant, which has an excellent selection of sake, and they've also opened a small restaurant/bar, Saku, that serves sake.
A little bit out of the city centre near the Letzipark sports stadium, Shizuku also has an online shop so you can order for delivery. Sign up for their newsletter or keep an eye on the site for occasional tastings or events with restaurants, cheese manufacturers, etc. Range as of June 2018 includes Shirayuki Banzaimon, Kachiumamai, Daihoju, Ōtegara, Itami Morohaku, Shirayuki Edo Genroku and Shirayuki Akafuji (Konishi Shuzō), Manyo Yamatsuru (Nakamoto), Heavensake, Kozaemon (Nakashima), Inatahime, Goriki and Iku's Shiro (Inata Honten), Sawaya and Kuriyazake (Matsumoto), Karaku (Shotoku), Fukugao Whisky Barrel and Fukugao Bourbon Barrel (Fukugao), Asahimai (Masuda Tokubee), Miyabi and Tarusake (Kiku Masamune) and Gekkeikan.
This Japanese-inspired chain has a very limited selection from Ninki Shuzō, Richie Hawtin's Enter Sake, Kizakura and Nihonkai (Shirobuta nigori). Worth checking for their changing guest sake, currently (June 2018) Masuichi Square One. Many locations in Zurich, and the Bellevue restaurant does a very good tasting set.
Limited selection mostly from large (mass-production) breweries, but convenient in an emergency and sometimes have interesting smaller brewery bottles. Selection changes occasionally but usually have 300 ml bottles of nigori, carbonated sparkling sake and junmai, and a larger range of larger bottles.