Most onboard motherboard raid chips run off of the PCI bus, so the performance difference is going to be minimal.
Currently, I have both an IDE Raid card and a SATA Raid card installed and both give very good performance. Although, one thing to note is that it was a bitch to set them up properly so that they could both be detected in the bios. Actually, right now my bios doesn't see my IDE Raid card at all, but it still works in windows. Can't boot off of it, can only boot off of the sata drives.