Perhaps Asakusa if you go early to avoid crowds and then over to Ueno for the Park or Market to the excellent snack shop Niki no Kashi for snacks to bring home. Or you could go to Sky Tree and there's a branch of the snack shop there, too. If you like kitchen goods then Kappabashi district in Asakusa is fun to window shop. If the weather doesn't look good then possibly check out Azabudai Hills for the architecture & a bit of the posh vibes. You might want to check out the TeamLabs exhibit there (advance reservations highly advised). I'd finally go over to Mont Thabor bakery in Azabu Juban for the milk bread.

There's other wander-able neighborhoods though there's a bit of a running joke these days that you need to spend 1,000 yen in Tokyo to find a seat when you get tired. I totally felt that in Shibuya my last trip where a usual trick of finding a department store's upper floor rest area yielded absolutely no seating.

Personally, I might actually spend the extra night in Kushiro if I could get in more winter sushi or if I had enough time, stay at Yoroushi again where they have Blakiston fish owls https://yoroushi.jp/en/ (I'm not a birder though a friend is) I got the sense that other birders were staying there to get a lifer (we did see one).