Colorful manhole covers with animation characters or other objects that have connection to the locale is another "Only in Japan" thing. Some of them are in major tourist zones like Ueno Park or Shinjuku. Others are in more residential areas, so it provides a reason to visit the less touristy parts of the city. All of the spots mentioned on this page can be easily accessed using the public transport.
The Tokyo Metropolitan Government Bureau of Sewage has a very detailed page about the different designs.
Within central Tokyo
Sumida Ward - Nearest station: Ryogoku Station (JR Sobu Line or Toei Oedo Line)
Ryogoku is known as the town of sumo and also the birthplace for Katsushika Hokusai, the ukiyo-e artist known for woodblock print series "Thirty-Six Views of Mount Fuji".
There are two near the west exit of Ryogoku and a third one outside the Sumida Hokusai Museum, about 10 minutes away.
Taito Ward - Nearest station: Ueno (JR Lines, Tokyo Metro Ginza and Hibiya Line)
There are two Pokemon-themed manholes inside the Ueno Park, one next to the National Museum and the other next to the National Museum of Science and Nature. Both are to the left side of the main entrance.
Related URL: https://local.pokemon.jp/manhole/desc/173/ https://local.pokemon.jp/manhole/desc/172/
Chiyoda Ward - Nearest station: Ochanomizu (JR Chuo and Sobu Line), Jinbocho (Hanzomon, Mita, Shinjuku Line)
There are three manholes themed on characters from Osamu Tezuka's "Astro Boy" manga series. The name Professor Ochanomizu is taken from this area, and in the story Astro went to Ochanomizu Elementary School. They are all on Meidai-dori, the large street that runs south in the direction of Jinbocho, the district known for its used book stores.
Shinjuku Ward - Nearest station: Shinjuku (JR/Tokyo Metro/Others)
There are two Godzilla-themed manhole covers in front of the Shinjuku Toho Building which contains the Hotel Gracery and the Godzilla head on the corner of the tower.
Shinjuku Ward - Nearest station: Sendagaya (JR Sobu Line), Kokuritsu Kyogijo (Toei Oedo Line)
Along the sidewalk on the northern end of National Stadium, there are several Tokyo 2020 design manhole covers with different color patterns. The stadium was rebuilt for the Summer Olympics and will also be used for the World Athletics Championship scheduled to take place in September 2025.
Along the Odakyu Line
The Odakyu Train originates from Shinjuku and runs through the suburban area of Tokyo on its way to Hakone Yumoto. There are three stations along this route that have a concentration of special manhole covers including Machida with six Pokemon-themed covers.
SOSHIGAYA OKURA STATION is in Setagaya-ku, so it is still within central Tokyo. It is about 25 minutes on a local train from Shinjuku (Express does not stop). The entire neighborhood is themed after Ultraman, as the Tsuburaya Production originally had its office nearby. There are five Ultraman-themed manhole covers, all within a short walk from the station.
There are other Ultraman-themed objects near the station and also a shop "Shot M78" that is open from 11-17 (Closed on a Wednesday)
Related URL (with map): https://www.city.setagaya.lg.jp/03647/4990.html
MACHIDA STATION is about 30 kilometers away from Shinjuku but can be reached in about a half hour with a rapid express train. Another 10 minute walk from the station is Serigaya Park 芹ヶ谷公園 where all the manholes are located. Access to park will require going down long stairs.
Related URL (with map): https://www.city.machida.tokyo.jp/shisei/city_promotion/pokemonmanhole.html
TAMA CENTER STATION, 40 minutes from Shinjuku on a Tama Line express train, a route which branches off the main route at Shin-Yurigaoka. Also can be accessed on the Keio Line, a different company train that also originates at Shinjuku.
This is the center of the Tama New Town residential area and also home to Sanrio Puroland, the theme park dedicated to Hello Kitty, My Melody and other kawaii characters. There are several versions of the Hello Kitty manhole near the Puroland and around the Tama Chuo Park south of the station.
Related URL: https://www.gesui.metro.tokyo.lg.jp/pr/kouhou/designmanhole/tama