End your trip high above the city lights
Hakodate, Kobe and Nagasaki are known for Japan's three great night views, each seen from a mountaintop where you look down on a city spread between hills and sea. Ride up a little before sunset and watch the city slowly light up below you. Hakodate and Nagasaki are a flight away from Tokyo, while Kobe is close to Osaka, so it is the easiest one to fit into a trip.
The 334-meter summit of Mount Hakodate, at the southern tip of Hokkaido, looks down on a city squeezed between two bays, so the lights curve along both shores. A ropeway takes about 3 minutes from the base to the top. From sunset on there are lines for tickets and cars, so go up a little before dark, and note that the ropeway stops for inspection for a period each year.
A lookout 702 meters up Mount Maya, above Kobe, where the lights of Kobe and the cities around Osaka Bay spread out below. Its name, Kikuseidai, means a place where you can scoop up stars, from the feeling that the sky is close enough to touch. You get there by cable car and then a ropeway, and the lookout itself is free.
The 333-meter summit of Mount Inasa in Nagasaki, reached in about 5 minutes by ropeway. From the observation deck, the lights of the city fill the valleys between the hills and line the harbor below. The ropeway sometimes stops for inspections, so check the operator's notices before you go.