"Miracles" is one of the most unintentionally funniest videos ever. However, Weird Al is the most consistently (and intentionally) funny music video makers ever.
As for just greatest, Chris Cunningham has my
deep dark twisted soul heart.
To point out a couple of music videos that fit right in the middle of great and funny, are two grossly underrated ones by Mercury Rev from the BOCES album:
http://www.youtube.com/watch?v=8h2VvMgwIF4NSFW! No actual naughty things shown, but certainly implied. I mean, Ron Jeremy is in the video. However, I love how Mercury Rev in one fell swoop achieved something that Hawkwind were trying for years to get close to: Pure sonic space sleaze. "Something For Joey" is also their best song.
An actual safe for work video is Mercury Rev's "Bronx Cheer", which is much poppier, with a video filled with kids in a playground
http://www.youtube.com/watch?v=6JQ_oxYEQpABoth videos can make you dizzy, though.