Your friend needs to read up on Tokyo and decide what he wants to see. Your question is something like asking, "My friend is arriving at LAX on Saturday night and leaving on Monday morning. Where should he stay and what should he see?"
And you'd think, "Wait a minute, downtown LA, Malibu, Santa Monica, Disneyland, Universal Studios, the Getty Museum, and you have only one day..." So you'd tell the person to read up on these attractions, look at a map and a guidebook, and figure out what his priorities were and what he could reasonably see in a day.
Now keep in mind that Tokyo is even bigger than the Los Angeles area, denser, and made up of more distinct neighborhoods.
If you're not in a backpackers' hostel, cleanliness is a given, and if you're not fussy, the business hotels, for less than $100 a night, are just fine and located all over the city.