If you are in Tokyo and you have only one day to visit Kyoto, then take a bullet train (Shinkansen) from Tokyo (or Shinagawa) Station to Kyoto Station.
Tokyo to Kyoto Bullet train
Shinkansen bullet train runs almost every 5 minutes during day time. So you never miss one. There are three types of categories of Shinkansen. You should take Nozomi Express and avoid Hikari and Kodama. Hikari and Kodama stops at many stations between Tokyo and Kyoto, and takes more time than Nozomi.
If you take a Nozomi departing from Tokyo at around 7:30 am, you can arrive at Kyoto Station by 10:00 am. You can leave from Kyoto to Tokyo, after dinner.
From Tokyo to Kyoto one day model plan
8:00 am: Leave from Tokyo by Shinkansen Nozomi Express 207
10:15 am: Arrive at Kyoto Station
10:15 am: Join in the “Private Kyoto Tour” or a similar tour from Kyoto Station
Go around Kyoto with a guide for 8 hours
18:15 pm: End of the tour at Kyoto Station, take dinner around Kyoto Station
19:21 pm: Depart from Kyoto to Tokyo by Shinkansen Nozomi Express 444
Tours in Kyoto
If you are familiar with transport in Kyoto, you can visit various places by yourself. Nowadays, Google Map can tell you how to reach to next destination, although the bus network is very complicated in Kyoto.
If you are not very sure where you go, or how to take public transport, then consider joining in a packaged tour. There are so many Kyoto highlight tours for a day.