Some things in Master's philosophy of Unity may be construed as Marxist thought, but was it portrayed so in the game? Master's headquarters are at a CATHEDRAL, there is a room with the PEWS in Master's headquarters, and his disciples wear monastic ROBES. If the Master's Unity was supposed to represent any sort of Communist or revolutionary movement, there would be slogans on the walls Calling for all sentient beings of the Wasteland to Unite, Supermutants would have Commissars and the Master would be calling himself the Chairman or the Secretery General or something.
Communism might not be the intended ideology of the Master, but there is another possibility. In most of the world's mystical teachings there is a striving for the Unity of the Spirit, where the worshipper gives up his own individual soul/identity to merge with the Universal soul. That is also known as Unity, and is the basis of teachings in most modern cults.
Fallout is set in California, and California was known for both, revolutionary politics and new age philosophy. I think that the New Age is the inspiration for the Master and his Cathedral. Revolutionary politics is also represented in Fallout, but I saw the reflections of it in Adytown and in beret wearing Set in Necroipolis, who carried himself with the revolutionary chique of Che Guevara and the Black Panthers.