Certainly the "Manalishi" - "Maharishi" similarity seems obvious, though I don't recall ever seeing an interview where Peter was asked about that specifically.
Of course Peter's family name is Greenbaum, not Green - but I think you're right that Peter's using the word "green" in this song title seems very intentional. "The Green Manalishi" was not the first song where Peter made deliberate use of the word "green". Remember "Show-Biz Blues", where he sings:
You're sitting there so green
believe me, man, I'm just the same as you
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