It took a while to explain gluten free and cross contamination to the waitress and chef. We used Google translate. The chef told me their rice vinegar has wheat, so he gave me plain white rice without rice vinegar. He also prepared some raw fish on a cleaned surface. Their green tea is also gluten free, but may be susceptible to cross contamination as the powder is in a self serve jar on your table.
Like any sushi restaurant in Tokyo, if you bring your own gluten-free soy sauce packets (like I do when I’m traveling) you can eat just about anything on the menu here. Just avoid the obvious (like the fried chicken karage) and things with sauce (like the unagi) and you’ll be fine.