I found Yogen-in to be a real hidden gem that was not crowded but also not off the tourist path; it's just a minute's walk from Sanjuusangendo!
Yogen-in Temple is small, but there are two main reasons to visit. The first is to see the famous paintings of elephants and other animals by Sotatsu Tawaraya. These are very well-known and recognizable images in Japan, and they are unique Buddhist works.
The second reason to visit is to see the ceiling! The ceiling was constructed from the floorboards of Momoyama Castle, which was the site of a fierce and bloody battle. On the ceiling of Yogen-in, you can see outlines of bodies in blood from the seppuku of Mototada Torii and his men. One of the outlines is particularly clear that it is a person. It's quite fascinating!
Entrance is 500 yen. They require all visitors to be guided through the temple in Japanese. Because of this, they sometimes disallow foreign visitors from entering. If you speak Japanese, even a little, you should be able to enter easily. Others may still be able to enter, as well. I knew Japanese, so I was permitted to enter, but I've heard mixed reports from those who do not know it about being able to enter or not. If the temple intrigues you, I highly recommend trying to enter!