If you look at this thread you can get a clear idea of how the analysis evolved over the years and that as of now it might not be a very good ploy to use ChIPSeq peak calling for the same.

It depends what you are interested to find. I have no idea of RIP-Seq but this is what I found might be useful. So it is usually dependent on the IPed protein. Having said that take a look at this thread and this link (gives quite a number of tools for RIPseq analysis)