The most peaceful place I've found while living in Yokohama is Shomyoji Temple near the Kanazawa-Bunko station on the Keikyu rail line. The structures and iconic red bridges have been rebuilt in the past century, but the site has been used as a temple and library since the 13th century.
Flowers bloom in waves throughout the spring, summer and fall: cherry blossoms, irises, hydrangeas and red spider lilies. Wildlife include koi, so many turtles, restless frogs and a beautiful gray heron that nests on an island in the pond.
Behind the main hall rises a hill with trails. The top has great views of the Uminokoen beach and Hakakeijima Sea Paradise to one side and the skyline of downtown Yokohama and its Bay Bridge on the other side. If you're lucky and the sky is clear, you can peak through the trees to see Fujisan to the west.
Signs in English point the way to the temple from the train station. Entering the temple grounds is free, and the library charges a small fee to see its museum with rotating exhibits.