The traditional Japanese diet is very healthy, it includes: fish, meats, eggs, fermented vegetables, broths, and seaweed. Well when I went 2 years ago, I was shocked at the amount of junk food you see in the street (vending machines with sweets and sugary drinks) and the amount of stalls you see selling sugary treats you see the younger generation eating. This showed me that the younger generation are not truly eating their traditional diet and many of them are overweight unlike the elderly you see.
There was a language barrier when It came to reading menus so I had to do my research where to eat!

Where I ate
1. Sushi Ouchi
I had to find a good traditional sushi restaurant that was not serving cheap and quick sushi. Thankfully I found this gem! This was the highlight of our trip, the owner which is also the sushi chef and waiter were one of the nicest people we ever met! They only serves wild caught fish, non GMO miso, organic rice (with no added sugar or MSG), naturally dried sea salt and free range eggs.
FYI, they only take cash.
Address 2-8-4 Shibuya, Shibuya-ku, Tokyo +81 (03) 3407-3543
2. Le Pain Quotidien
Good option if you are looking for food more familiar to you, we went for breakfast and had an egg dish. It's not as good as LPQ in the states or Europe but it was nice to have the option there.
3. Revive Kitchen Three Aoyama
Trendy & modern atmosphere. This place is great if you are looking for gluten free options (pancakes, bread, and pasta made from rice). The pancakes and avocado toast with added eggs is delicious. They also have green juices.
4. Elle Cafe Aoyama
Very chic atmosphere. They use organic ingredients and have gluten free options.
5. Natural House Aoyama Organic Market
Good organic market if you are looking to buy fruits, veggies, or snacks. They also a juice bar and prepared food for on the go. All the stickers were in Japanese so it was hard to be able to read the ingredients of the products.
I'm sure there is a lot more healthy places to eat in Tokyo but in the few days I was there, these are the places that I stumbled upon.
Enjoy!!! Tokyo is a great city :)