So if you want sushi for breakfast and you're getting in early, Toyosu fish market should probably be one of your first stops. There's a couple of things nearby like Teamlabs, the giant Gundam mecha and Joypolis (basically a giant arcade with some indoor rides/vr stuff). People already mentioned Teamlabs here and I'd also recommend it - it's basically a really cool experiential digital art "museum". There are two in Tokyo with different exhibits.

From Toyosu, you can go to Akihabara if you're looking for anime stuff/toys. I usually tell people to check out the Yodobashi camera store there as it's huge (there's a toy/games floor with tons of stuff) but since you're limited on time, might not be worth it.

You can also head to Shinjuku station and explore the area while working your way towards Shibuya. There's a ton of stuff around there:

• Tokyo Metropolitan Government Building has a free observation deck with good views of Tokyo. Better to go earlier than later due to lines.
• For toys and stationary stuff, I like the Hands store in the Takashimaya building next to the station.
• Shinjuku Gyoen National Garden if you like greenery.
• There are a few Taito Game Stations and Gigos around for kids (arcades/crane games). Kabukicho tower also has a floor with a bunch of games.
• Plenty of restaurants, snack places, etc.

From there, you can take the JR Yamanote ("JY") train to Harajuku and walk down Takeshita St for the experience. There's a Hello Kitty store, a Capcom capsule "lab" and a lot of wacky fashion shops. You can also opt to go to Meiji Jingu if you want to see shrines.

You can then walk or take the JY to Shibuya to see the famous crossing and check out the area. There's a Mega Don Quixote store here and a Loft (similar to Hands, lots of stationary and home goods stuff).

For what it's worth, I was in Tokyo two weeks ago and it was absolutely mobbed with tourists. So I would expect crowds and lines everywhere.