Weka 3.7 has new packages for distributed processing in Hadoop. One of the jobs provided by these packages will compute a correlation (or covariance) matrix in Hadoop. The user can optionally have the job use the correlation matrix as input to a PCA analysis (this part runs outside of Hadoop) and produce a "trained" Weka PCA filter. This scales Weka's PCA analysis in the number of instances (but not in the number of original features since the PCA computation still happens locally on the client machine).
For more info on the Hadoop packages see:
http://markahall.blogspot.co.nz/2013/10/weka-and-hadoop-part-1.html
The distributedWekaHadoop package can be installed via the package manager in Weka 3.7.
Cheers, Mark.