Watsuki and the Sony animators drew a lot of their inspiration for their scenes of Tokyo from Meiji-era prints and photographs. You can see a lot of well-known landmarks. But beware – some of them either weren't there yet in 1878, or looked very different.
For centuries, the center of Nihonbashi has been the "zero milestone" for measuring distances from Tokyo. The bridge shown in the Kyoto arc is the present-day structure, which was actually built in 1911. Kenshin's Nihonbashi, seen here in a print by Kiyochika, was much plainer. I have found no information about this bridge; it is obviously of Western design and replaced the traditional Japanese bridge shown in earlier prints by Hiroshige, but I don't know when it was built or why it was replaced. It may have been destroyed in a catastrophic flood that submerged much of Tokyo in 1910.
This elaborate hall for state receptions was not completed until 1883, despite its appearance in the third-season filler episode about Yahiko's princely double. The Japanese government built it to house and entertain visiting Western dignitaries, but its "high-collar" (fashionably Western) glory was short-lived. In 1889 it became a private club, then an insurance company office, and it was finally torn down in 1941.
Ginza had been a modest commercial district until one of Tokyo's periodic fires destroyed it in 1872. The government decreed that new construction must be fireproof, and hired an English architect to rebuild in brick. Printmakers turned it into a showcase for Civilization and Enlightenment – though the people who actually lived and worked in the stuffy, damp, mildew-ridden, and expensive buildings were far less enthusiastic. This print is actually somewhat later than the red-brick Ginza of Kenshin's day.
Iron bridges were seen as being particularly "civilized and enlightened," and a number of Tokyo's wooden bridges were replaced by iron ones in Meiji. I think this is the one we see Kenshin crossing in the first-season ending credits. If so, it's an anachronism, as the iron Azumabashi was not built until 1882, though as the print shows, it was a well-known Asakusa landmark until 1923, when its wooden floor burned in the firestorms that followed the Great Kanto Earthquake.
This used to be one of the busiest places in Tokyo, the terminus of the rail line to Yokohama (and later, another line that ran west to Kobe). The station is gone now, replaced as the Tokyo rail hub in 1914, and torn down or destroyed in 1923. No plans or detailed descriptions survive, but the exterior was pictured in countless prints and photos. The station in Yokohama was a near twin.