RNA-Polymerase III transcribed genes
GO is based on experimental evidences; biomart is quite good. GO:0006383 seems to be the right tag.

If you want to use the ChIPseq data then you can do this:


Map the ChIPseq reads to the genome. If you already have the tracks
then you need not do the mapping. You would have the position of the
reads in the genome.
Now count the number of reads mapping to each geneic region. The gene boundaries can be obtained from a GTF file.
Optional: Normalize the reads with the length of the gene.
Find the difference between the number of Pol-II and Pol-III reads for each gene. 


By doing this you still won't be able to say that "gene-x is transcribed by pol-III". All you can say is that "pol-III binds to that geneic region". If there is an even distribution of the ChIPseq reads along the gene then you can assume that there is an active transcription and the polymerase is not merely stalled. You can also do a CLIP (Crosslink-Immunoprecipitation) of Pol-III followed by a RNAseq. This will enable you to find RNAs transcribed by pol-III (this is a better way than ChIPseq but I don't think anyone has done it yet; so no ready data).