I recently learned about this portal for those craving vegetarian low carb and gluten free meals: https://vegewel.com/en/ and also offers many other useful information for foreign travellers such as: availability of english Staff and menu, etc.
But I am no expert of healthy this or that and if you seek a local expert you can find her here: https://www.erica-angyal.com
And take it one step further: https://airkitchen.me/list/tokyo.php visit air-kitchen-plus allows all types of cuisines (vegetarian and vegan, etc.) for travellers from all around the world to book and eat home-cooked Japanese meals for vegetarians and vegans made by authentic Japanese hosts in their homes.
But if you search the pièce de résistance it is non other than Brown Rice a very stylish restaurant located in Omotesando Street. The owner is not only interested in vegetarian but in all those good things in life: https://www.nealsyard.co.jp/brownrice/welcome/
There is also Ta-im an Israeli restaurant in Ebisu area serves Israeli cuisine, hummus and falafel and offers options for vegetarian and vegan. Some of spices and wines are directly imported from Israel.