What do you like to do while in Tokyo when not working? Staying near that would save a good bit of time and train squeezes during commute hours.

As you said, there are a lot of hotels. Perhaps you're looking more for a list of value-for-money Japanese business hotel chains which would be comfortable for working in? My national chain favorites other than Tokyu Stay include Dormy Inn, Richmond, and Daiwa Roynet. I haven't been tempted by a Dormy in Tokyo, though a few have opened since I last checked https://www.hotespa.net/dormyinn/list/tokyo.html. A friend likes the Toyoko Inn chain as it fairly consistent and clean. I've also found JR line hotels to be pretty good value & close/attached to train stations. Looks like JR East opened Hotel Mets on top of Akihabara Station including two room types which have a balcony (but backless stool instead of backed chair for mini desk or small side table + mini couch)

I'm also a Tokyu Stay fan. For those on a budget who want to be on the East side, the Shimbashi location isn't too far of a walk from the station and Shimbashi station is well connected. The surrounding food options are open a bit later for salary men which would probably be comfortable for solo stays for those who prefer to eat out. "Residential" rooms also come with a hot plate & few basic cookware for cooking in room. Most room categories also have microwaves and basic dishes + cutlery for leftovers or take away vs normal business hotels with shared hallway microwave & no cutlery.

Tokyu Stay Premier Ginza near Higashi Ginza station is a quick walk to the subway station which connects underground to Ginza and Hibiya. It is across the corner from the Mitsui Garden Hotel and a few other hotels have opened up in that area like Super Hotel Premier Ginza, AC Hotel by Marriott, Courtyard by Marriott, and Agora Tokyo Ginza. There's plenty of food options including department store bento for those on budgets (or prefer not to eat-in & not combini), though IMO it does run towards the more gourmet side. It is on the pricier side compared to some of the other Tokyu Stays as it comes with a few extra toiletries in the lobby and daily cleaning option (at least pre-covid). I'd also say that while the location is close to the shopping of Ginza or a quick subway ride to Nihombashi, it can feel a bit corporate, crowded, or overly touristed.

Kinshicho's been on my list of areas to look for a hotel as it has a lot of activity but a little less touristed. It's near a Seijo Ishi and has a lot of food & shopping options. https://www.flyertalk.com/forum/33337468-post12.html Er, I admit I go there for the several rather large 100 yen chain stores.

Tokyu Stay Takanawa opened up a few years ago and is right by Sengakuji station, ~ 8 min walk to the new Takanawa Gateway station on JR Yamanote & Keihin Tohoku. The neighborhood looks to have a more residential feel x larger than average JP biz rooms (18 - 23 sq m) which is what I'd be looking for on extended Tokyo stays with WF Hotel time, especially if working in a US time zone so I could enjoy a daily walk without too much crowding. Many of the core tourist district single hotel rooms are between 13-18 sq m.

My personal preference is for more slightly quiet residential feel when I have time to enjoy a neighborhood and not a lot of specific sightseeing/shopping to do. I'd appreciate recommendations for apartment hotels in such neighborhoods. The Monzen Nakacho location is older but near Ito Yokado Kiba. Toyosu to Ariake has also oddly been on my neighborhood list, despite being industrial and former Olympic village area, thus not "cute" but near Aeon Shionome & Muji Ariake. There are a few new hotels and resorts in those areas, too, but may add commute time and not what you'd consider good metro line.

If you'd be open to biking Looking for another great neighborhood to stay