No question its an apples / oranges question like asking which drug is responsible for better music - cocaine or heroin. Interesting debate, but there can't be a definitive answer.
As has been mentioned, Zeppelin's influence was broader, while VU influenced a select few with a big impact.
I think VU introduced an element of music as "modern art" which I'm not sure existed before them. That's huge. And they were unique.
Zeppelin amplified the blues. As the Stones and the Who had done to varying degrees before them. Where does the Who influence end and the Zeppelin influence begin?
Each of VU's 4 official releases were completely different. Between them, they cover all the bases, and influenced a very diverse group of followers. From (for example) I'm Waiting for My Man to What Goes On to Sunday Morning to Sister Ray to the mellow come down of their third album to Sweet Jane to Rock and Roll . . . how many different genres did they inspire??
I suppose every guitar "wank" owes something to Jimmy Page. . . . but its like the White Stripes. Awesome band. New take on the blues. But its more of a link in a chain than an inspiration.
An interesting corallary question is who are the Top 5 bands influenced by each group? Zeppelin's would be who - Aerosmith, Guns N' Roses, Licensed to Ill era Beastie Boys . .who else worth mentioning . . Motley Crue? Van Halen?? Who else?? Seriously . . . Obviously the whole heavy metal scene of the 80s derived from Zeppelin, but what great bands has Zeppelin influenced that I'm missing.
VU . . .you can start w/ Bowie; Stooges; the CBGB scene; Modern Lovers; R.E.M.; Sonic Youth . . . everyone those guys influenced in turn . . .
Of course some bands must be considered influenced by both - Jane's Addiction . . .
I'm going w/ VU. They were a jump off point. Zeppelin, like Aerosmith, GNR and White Stripes are more of an endpoint . . . taking the blues to another place . . . but not really having a long or strong lineage following it.
