They may not have played the same kinds of music but there were some spiritual links to their outputs.
About 10 years ago (just before Sampleface was created), I was studying Sun Ra and found this article by Brian L. Knight for The Vermont Review. Legends Before Their Time: A Zappa/Sun Ra Comparison looks at the similarities and contrasts between the avant grade musicians.
There are two approaches to discover the music and personalities of Frank Zappa and Sun Ra. One is to collect their music, which is rather formidable task after discovering the size of their discographies. There is a selected discography at the end of this article to serve as an aid. The other approach is to read about their lives. There are three informative books in circulation that cover the amazing lives of these two performers. The first is Ben Watson’s Negative Dialectic of Poodle Play (St. Martin’s Griffin) which took a very detailed and scholarly approach to the music of Frank Zappa. Second, there is Space Is The Place: The Life And Times of Sun Ra (De Capo Press) which was Yale University’s American Studies/Anthropology professor, John Szwed’s chronicle of Sun Ra’s interesting and eccentric life. Finally, there was Frank Zappa’s autobiography – The Real Frank Zappa Book (Poseidon Press). The three books not only provided interesting glances into the musician’s lives but more importantly, their roots, their techniques and their impact on modern music.
The obvious connection between Zappa and Sun Ra is Madlib, who has sampled the pair extensively. In many ways, Madlib is a modern conduit for their music and ethos; pushing the boundaries of what music is and how it can be represented. And unique forays into jazz between the three.
I recommend you read the full essay and buy the books for further reading.