Part of the problem is that the metaphor breaks down: a paper is like an individual webpage, but a journal is like a company -- it has a much longer time-line, and its impact varies over time. Also, unlike web links, citations don't go away; they just accumulate over time. Since the point of these citation metrics are to rate the journals (and maybe the scientists), pagerank has some difficulties in the domain. It works better for ranking individual papers than for scientists or their journals.
This shouldn't be too surprising: TechCrunch (for example) probably has a good rank on many pages, but pagerank doesn't tell us anything about Michael Arrington's reputation.