I did some extensive research when I was in Tokyo last.
Tried 4 brothels and two "massage" services. Background: I'm Asian, fairly young, in really good shape.
Like others have said, all these places make you take a shower first. It's with the boy and actually quite nice. Don't let the soap sit for too long on you though; it's a germicidal soap and will dry your skin out, and even burn in one case, if it sits for more than a few minutes
A lot of these places will give you discounts if you visit between 12-5, if you visit during the week, etc. And you can also go through the catalog of boys when you're there.
Brothels -
TK - https://kids-jp.com/en/tk/
not gonna spell out the name because it creeps me out to have the second word associated with a brothel... saw three guys. They have some hot boys for sure! Kyoh and Yasutaka were both extremely hot and had amazing bodies but weren't the most enthusiastic. Isamu was very enthusiastic but didn't have as nice of a body. Very nice facilities and easy to get to in Shinjuku
Chance - https://chance-shinjuku.jp/cast/
did outcall for a threesome and incall for a 1:1. For the outcall, they brought every thing they needed. Shinji is a super hot young short top. He came with Ryuki who was very nice but wasn't a great bottom, the role I wanted him to be; he couldn't take my cock. Also did an incall with Shintaro who is suuuuper sexy. I took a chance on him because they didn't have his face unblurred on the site (they do now), and I'm super glad I did. Incall facilities are also very nice. Shinji and Shintaro both speak excellent English
An Independence - https://en.hi-na.com/cast/
Did incalls with them. Saw Yuito twice, Haruki once. Yuito is so cute and has a great body and really sweet. He's the stereotypical Japanese guy you see in Japanese porn that is super sensitive and moans when you touch him. Haruki was nice but didn't look like his photos. Facilities here were also really nice
DG - https://www.dgdgdg.com/boy/list.php?shop_id=10
saw Aoba for an incall. Very cute guy, can actually take a pounding. Saw Sakito for an incall. Absolutely gorgeous and cool and sexy and a good top.
"Massage Services"
Redline - https://www.redline03.com/boys/
Saw Keisuke for an incall. My 90-minute course got changed to a 60-minute because the owner had to push back the session by 30 mins and then I was 15 mins late. They say on the site that sex isn't an option during a 60-minute course but I thought maybe because they were the ones who pushed it back, that it could still happen. It couldn't. TERRIBLE facilities, exactly what you'd think a brothel would look like. Terrible massage. But Keisuke was indeed very cute and had a giant dick
Cream Men's Spa - https://creammensspa.com/
Pretty great experience. Owner was pretty accommodating and sent me profiles of guys not on the site. Did an out-call