I've only seen the two big ones, and I'm surprised by how difficult this question seems to be for people.
Because what is a comedy film for?
Brian certainly hangs together better.
Grail pushes the envelope of comedic filmmaking.
Brian has excellent sketches (Latin grammar lesson, The Judean People's Front, Blessed are the Cheesemakers, etc)
Grail has more excellent sketches (Witch trial, Knights of Nee, Sir Robin, Castle Anthrax, etc)
Brian is better directed
Grail is the punk rock comedy film
Brian has better acting
Grail has more laughs
And on and on.
I ask this question BECAUSE it is hard. So very hard.
And bless you to all those who still hold onto Meaning of Life. It deserves some nods.