I'm a longtime fan of both, and depending on my mood I can go with either duo on any given day. I look at it from two ways, one would be comparing their albums, the other would be comparing the catalogues. If we're going strictly off of albums, then I'd go with Mobb Deep.
Debut Album: Infamous versus Lord Willin; Gotta go with Infamous ( I don't consider Juvenile Hell their debut, same way I don't consider Exclusive Audio footage the Clipse debut)
Follow up: Hell on Earth vs. Hell Hath No Fury; That's a tough one, but I'm inclined to go with Hell on Earth.
3rd Times a Charm: Murda Muzik vs Till the Casket Drops; Murda Muzik easily, but that's not to say TTCD was terrible, but Murda Muzik had more bangers, plus gave us the Quiet Storm. TTCD was a bit incohesive, especially as a follow up to HHNF which was damn near a classic record.
Based off of those three albums only, I'd say the Mobb. Still, they fell off something terrible after Murda Muzik to the point I've never even bothered with their G-Unit joint. Still, when considering both group's overall catalogues, and I mean solo efforts and mixtapes, I'd run with the Clipse at that point. I loved Return of the Mac, liked HNIC (didn't care for part 2), loved Albert Einstein, and liked Free Agents. Didn't really care for Hav's solo projects.
On the other hand, I loved We Got It 4 Cheap vol 1, 2, and 3. The album itself was a bit lackluster, but those mixtapes were serious and better than most of the albums from artists during that time frame. I loved Push-Ton's Fear of God mixtapes. Loved the Hologram P collection that someone put together. Loved Road to the Casket Drops, loved Pusha's official debut, and can't wait for the follow up.
So again, on albums alone, I'll go with Mobb, but total catalogue, I'll go with Clipse.