AITAvision, which appears in several episodes, is ALTAvision (on Studio ALTA) in reality, located in the south of Shinjuku Ward, in the third block of the district of the same name, with the Mitsubishi logo changed to "Mitsubashi".
The cable-stayed bridge partly visible on Kaito Kuroba's and Aoko Nakamori's way home seems to be modeled after the Tsubaki Sakura Bridge (辰巳桜橋), actually located in the Kōtō Ward of Tokyo and connecting the districts of Tatsumi and Shinonome across Tatsumi River.
One shot in Episode 4: A Witch Sheds No Tears from across the river to the Tokyo Sky Tree is a real spot on a promenade at the Sumida River in the Asakusa District in the Taitō Ward, right next to the Tobu Line Sumida River Bridge visible to the left. This shot also exemplifies that the skyscraper Kaitou Kid used to skate to the Sky Tree, neighboring it, is completely fictional.
The distinct tower of the Ekoda Museum in that same episode, on the other hand, is based on the "Jack's Tower" in the Naka Ward of Yokohama again - just like it was in the manga (see above).
The place she confronts Kaitou Kid on during her time stop in Episode 5 also is a real (and famous) crossing in the Ward of Shibuya, especially identifiable by the Tsutaya Building (which was renamed "Sutaya" in the episode) to the right.
... and the Mysterious House is a dead ringer für the Haunted Mansion. The Tropical Land also features a castle extremely similar in architecture to the Cinderella Castle, both situated in the center of its respective parks.
The cinema Kaito and Aoko want to visit in Episode 22: Red Tear is a real cinema in the Shinjuku Picadilly Complex in the district and the ward of the same name.
The unnamed jungle Yaiba Kurogane and his father live in seems to be (intentionally) highly ambigious about what jungle or even where it could remotely be. Besides the rather generous surroundings, animals like Gorillas (from Sub-Saharan Africa), Tigers (having their habitat in continental Asia) and Jaguars (who usually live in Central and South America) seem to have their habitat there.
Onimaru forces his entry into the Kokkai-gijidō, also known as the National Diet Building of Japan in the district of Nagata in Chiyoda Ward of Tokyo to take over the government of the country and remodel the building in his image of a demon castle, which he uses throughout Chapter 17 - 61 (Yaiba Volume 2, Chapter 8 - Yaiba Volume 7, Chapter 2). So, yes, Onimaru's castle is technically a real building - as this, it's one of the more important places to pinpoint the location of the fictional Yaoya District and the mansion of the Mine family, since it's pretty close to the castle.
Sayaka, Kagetora, Gerozaimon Geroda and Namako-Otoko arrive in Tokyo at the Marunouichi Building of Tokyo Station (pre-renovation status) in Chapter 42 (Yaiba Volume 5, Chapter 3), which is also named as such. It's location is the Marunouichi District in Chiyoda Ward, Tokyo. They disguise themselves and instantly go to the Mine house by foot afterwards, implying that Sayaka's home is relatively close to Marunouichi - another hint that Yaoya Town is around Chiyoda.
