This is a popular temple complex in the heart of Kyoto. Though busy, one can find a quiet spot to meditate while gazing upon the gardens in this Zen temple which was founded in the year 1202. 

Konchi-in Temple is a sublime place to stroll and, though there are not meditation classes offered, it is often quiet enough that you can find spot to slip on a pair of sunglasses and meditate for as long as you wish. Definitely not one of the main tourist attractions and therefore perfect for meditation.

Founded in 1291 by Emperor Kameyama, this temple complex is very popular. However, perhaps because it is small and off on one side, the garden is generally not very busy and there are several spots to sit and contemplate the beauty and serenity of the place (albeit with people strolling by).

Arrange for a private zaken meditation session (getting hit by a wooden stick and all). 

For an accessible introduction to Zen meditation, this temple holds daily classes led by the American-educated vice-abbot.