While not strictly speaking a museum, Houston’s Rothko Chapel is a magnificent place. Founded in 1971 by John and Domique de Menil, the chapel is an intimate meditative sanctuary. Rothko was commissioned to shape the environment and produced 14 paintings. He worked closely with Philip Johson, the original architect, and later with Howard Barnstone and Eugene Aubrey as the building was completed. Not surprisingly, the chapel is considered on of the great artistic achievements of the 20th-century.
I think I echo a belief held by many others in saying the fully glory of Mark Rothko is best experienced in full submersion.
Learn more at The Rothko Chapel.