Among independent travelers, there is a route that is very popular for walking around to see the local streets and enjoy Japanese dessert/cafes at the same time. You will not be disappointed as Japan is famous for the variety and presentation of sweets and dessert you will be drooling for years event after going home.
Route as follows: Get off at Omotesando Station (Tokyo Railway/not JR) => Walk to Harujuku Station/13min~20min (and look around) => Walk into Meiji Shrine/10min~30min sightseeing inside the Shrine => Walk (or take JR train) to Shinjuku Station/30-40min walking.
Today we begin the walking/sightseeing route at Omotesando Tokyo Rail Station with a dessert/fruit tart shop that I went for breakfast (dessert already at 10am??!!)
Quil Fait Bon has been really popular these past couple of years among Japanese girls and office ladies. They have at least 10 different fruit tarts in store everyday, and their fruit tarts are lighter in taste (less heavy cream) with lots of fruits. On busy days, you have to wait 15-20min with a number ticket to get to the counter, so I really recommend coming here in the morning.
Quil Fait Bon near Omotesando Station do not have seating areas for people to eat there. We looked at the fruit pies/tart at their counter, and picked 2 to-go.
Quil Fait Bon also have seasonal limited edition fruit tarts, so when in Japan, make sure to save space in your stomach for those fruit tarts.
Address for Quil Fait Bon at Otomesando: 東京都港区南青山3-18-5
Map (From Omotesando Station to QFB):