We did 11 days in Japan in October, mostly Tokyo and a few days in Kyoto - loved it so much thinking about going back in 2024. Can’t help w/ the north islands piece, can make some suggestions for Tokyo. We’re eager to ski up north as well, please share your experience when you return!
For Tokyo, we based ourselves in the Shibuya area and would do again. Easy to get around on train and/or walking.
Restaurants can specialize in one thing like noodles (Ramen, Soba, Udon), Yakitori (grilled things on skewers, mostly chicken/parts), Tonkatsu (breaded/fried pork cutlet, Sushi and bars called izakaya’s which can offer a variety of these things.
Hotel - we stayed at Cerulean Tower Tokyu hotel and they have king size beds. If you book a room on the executive floors, it gets you access to the executive lounge on 35th floor where they serve light breakfast things in morning, then just tea/coffee/water/soda until 5PM, then cocktail hour w/ light bites, all complementary. (Cerulean Tower Tokyu Hotel | Tokyo Shibuya)
Food - all in Shibuya area, none are high-end places, Asahi on tap is a great pairing for most things.
Yakitori - place called Toritake - food is very good and it’s a great experience.
Tonkatsu - place called Maisen, several locations. (レストラン | とんかつ まい泉 | MAISEN) (menu .pdf https://mai-sen.com/restaurant/82debfe9e76d71ce58eb3bf7c770a15b.pdf)
Izakaya - name is Kokappo Ohashi Shibuya - should make a reservation, great experience.
Cocktail bar - recommend Bar Trench, in Ebisu neighborhood just one train stop away from main Shibuya station. Great cocktails & can try Japanese gin/whiskey/vodkas. (Bar Trench | Asia's 50 Best Bars 2022 | Ranked No. 25)
Ramen -
Nagi (英語ページ│株式会社凪スピリッツ), classic to fusion like pesto ramen
Shuichi (Ebisu neighborhood) - make a great curry ramen (https://www.5amramen.com/post/curry-ramen-tokyo-shuichi) (しゅういち - 乃木坂/つけ麺 | 食べログ)
Would recommend a tour by 5AM Ramen (https://japanko-official.com/5am-ramen-tokyo-ramen-tours/).
You can view their “best Ramen” list @ https://www.5amramen.com/blog/categories/best-ramen-lists
For restaurant reviews, popular site Japanese use is called Tabelog (not Yelp/TripAdvisor) per one of our guides (Restaurant map [Tabelog])