The real world location for the events in the anime D.N. Angel was based on "Azumano District in Tokyo"
According to this Post about Dark Mousy:
Dark Mousy was the greatest phantom thief. Last appeared 14 years ago, disappeared suddenly, and then now he's out wreaking havoc around the Azumano District of Tokyo as he did for centuries. Nobody knows where he's from, nobody knows who he really is, and nobody knows what his real purpose is behind stealing all the artwork from various museums. Dark is some what immortal since 14 years ago. He was intiated in a ritual with Daisuke Niwa 14 years ago to become immortal. The bad part of the ritual was Dark would be in a coma state inside Daisuke's body till he turned 14. Dark's rabbit, Wizu, watched over Daisuke till he was able to transform into Dark. Dark is Daisuke half the time, to protect him and vice versa.
Likes: Ramen, Flying
Dislikes: People who don't know how to shut up, Pets
A small cozy apartment near the shores of Azumano.
When you search about "Azumano clock tower"
Clock tower is in the first episode.
(Remember the first episode where dark returns after 40 years and steals the bird symbol on the clock tower)
You would see google search results about D.N. Angel FanFics (Fan Fictions)
You'll notice that most of these talk about the Azumano District in Tokyo (or sometimes Azumano City)
Here's an example, although this is more like a retelling of D.N. Angel instead of a Fan Fiction
Also a comment on This Post about D.N. Angel also states that:
The location of where D.N. Angel takes place is hard to figure out,
but it is revealed in the last episode, on a box (that was as late as
I noticed it); if you translated the small bit of Kanji and Hiragana
written on the side of it, it came out to be "Azumano District
Reception", meaning that the town or area that the anime took place in
would be Azumano.