Taxi Fares

Do you what is the midnight charges for Taxi?

And how much is per KM?

There is typically a 20% surcharge between 22:00 and 5:00.
http://www.japan-guide.com/e/e2021.html

The fare depends on the taxi company, size of car and region of Japan. It is typically around 600-700 yen for the first two kilometers and increase by roughly 100 yen for roughly every additional 500 meters traveled. The cost also increases when the taxi is not moving for a prolonged time.

Hi Uji, thank you for your information.

Will it be the same if i take from Airport?
Coz my flight reach Haneda Airport at 12am. Should I stay near airport or Tokyo town?

Will it be the same if i take from Airport?

Basically yes. Sometimes airport taxis offer fixed rates for certain destination, which can be a relatively good deal. Also, if you use expressways, you will have to pay for the tolls additionally.

Coz my flight reach Haneda Airport at 12am. Should I stay near airport or Tokyo town?

I recommend to stay near the airport.