This map might be of some help. Looks like the harbor might be at the south (? There's no compass rose, so can't really be sure it's south...) end of the city. At any rate, it's down river from the Pizza Cat. In KNT, many of the place names given seem to reflect actual places in the real-world Edo/Tokyo, so studying the geography of that area might be benificial.
Off topic: I just noticed something really interesting about that map. Several of the characters are talking about a treasure hidden somewhere in Edoropolis. Seems like this might have been part of a promotional contest... since this map was originally 3 parts, each included with one of the "Mega Up" model kits, it might have been something along the lines of "collect and assemble the map, read the clues, and find the location of the hidden treasure!" Maybe if you sent in the correct answer on a postcard you'd win a prize, or something. Anyway, the characters offering clues are:

"It seems that the treasure is at a place that sells food."

"Looks like the treasure isn't at the pizzeria."

"At the place the treasure's hidden, it seems there's a girl who recently made a debut in the entertainment business."
My conclusion: The treasure's hidden at Omitsu's tea shop.

"Seriously!? Wow, Omitsu's riiich!!" *missile volley*