I guess i'd go for Zappa as a consummate musician and composer - very much in total control of his musical output and way ahead of the pop musical pack. Dan Van Vliet, Beefheart, on the other hand, is a more intuitive performer - a free form surrealist of sound.

They are both worthy of a place in the higher ranks of the musical pantheon.
Favourite album... well "Hot Rats" of course... bringing the two together.

If you think that one's good, you should also check out Bongo Fury. Also here's a version of Orange Claw Hammer with Zappa on guitar.

Zappa, mainly because he did so much more, his music is much more coherent and fluid which I prefer to the crazy, odd time signatures and just overall weirdness of Beefheart. I also think Zappa is more versatile in that he can seamlessly switch between any sound and release some really definitive recordings of that style. I still haven't heard an album quite like Hot Rats, and that's probably the best I've heard from either artist.

For Beefheart, he sort of established his own brand of music more than almost anybody. Whereas Zappa is very conventional in the sense that he always sort of made music in a previously established genre, Beefheart is the exact opposite of that. They're both geniuses, but Beefheart even while being significantly less skilled a musician and less prolific is somehow ironically the more innovative in the music industry.

They were both geniuses, they were both perfectionists, but yeah Zappa's my pick.

Also, didn't notice the last post in this was from 2014 - it was hanging out near the top like someone had just posted in it. My bad if that's a no-no.

I like Zappa a lot but over half of his material is too contrived to handle. Beefheart is a unicorn, he doesn't even have to try.

You fail the test when you go too far in the other direction. Zappa has a lot of excellent stuff, just no filter.

Here's one that everyone seems to forget about