I can't speak for the punkbuster issue (not sure if MW2 or Black Ops use it on PC, but Bad Company 2 does and I didn't have a problem there). But I had no issues with MW2 and Black Ops on PC. Granted, most of my time playing both was around launch and cheaters could have formed since then. many hours I played Black Ops, only ran into two people cheating. As for which is better, um, black ops has dedicated servers but I never had a problem with MW2 peer to peer stuff.
Personally I enjoy Black Ops multiplayer more, but that's just a personal preference than saying one is a better online experience.