Magneto lost to Thor in the 60's, but after Magneto's resurrection by Eric the Red Magneto's powers took a quantum leap and he could defeat all of the new X-Men including Phoenix. When Magneto faced the Avengers in that SUPER-VILLAIN TEAM-UP (or was it CHAMPIONS?), Magneto hurled Thor, Cap, and Iron Man away. Magneto manhandled Wonder Man. I've seen changes where Magneto can't effect Cap's shield or Iron Man's armor directly, but I'm not sure it would be easy for Thor to drain Magneto since his resurrection by Eric the Red.
and modern day Magneto has shown the ability to control the Hammer. If Thor can keep control of the Hammer then he "should" win more often than not but if he can't then he loses. Overall Mags wins 7/10. I believe mags does far worse against the Surfer and would be lucky to win more than 2/10 against him whereas Thor beats the Surfer 7/10.