The Captains last two albums were a return to form, Ice Cream For Crow, and Doc At The Radar Station. Lets be clear about beefheart he is a one off. His lyrics are genuinely extrordinary. He uses 2 lead guitarists but not in a Thin Lizzy style. No pedal effects just 2 players scratching and picking for attention. these 2 albums are probably the best SQ wise. I love him but only 1 album at the time.
John Peel said he was the only genius in rock music.
Dont Know much of Zappa's work but he did produce Beefheart's Trout Mask Replica.