In Shinjuku, these areas are right outside the Kabukicho exit, in front of Alta (with the large TV monitor overhead) next to the fruit shop, and outside the west exit.
When and where is the best place to hook up with someone in Tokyo?
Most establishments are open until 5am, and places like Izakaya and Karaoke often have a flat fee for all-you-can-drink / sing / party until 5am.
While I don’t recommend going to an izakaya for the sole purpose of hooking up with someone (unless you’re bringing that someone there), if you are already there with friends you might just find a table of friendly people (or a cute girl/guy on the way to the bathroom) who you can meet and share laughs with.
Whether their night was a success (drinking with their friends) or a feat of endurance (watching the clock until the boss stops drowning them in shochu and forcing them to listen to rude jokes), the transition to last train usually has people in a good mood.
In the smoking area near the Kabukicho exit of Shinjuku station, near 109 and the scramble crossing in Shibuya, and outside the East and West exits of Ikebukuro station, you’ll see the nanpa-shi (pickup guys), standing guard with their standardized uniform – gelled hair, man purse, loafers, and phone in hand – eyeing women from their sentry posts along the main pedestrian thoroughfares.