I'm not going to tackle the issue of what lipids are more causally related to plaque formation in the arteries; for that I would suggest you consider reading Dr. William Davis' blog (www.heartscanblog.org).
Recently there has been discussion as to whether niacin is beneficial for cholesterol or cardiovascular risk. One specific study suggested that niacin might increase bleeding risk when combined with statins. My understanding is that without the statins niacin poses no risk, so the issue seems to only be when it is combined with statins.
Regardless, there is an excellent article tackling the issue of niacin's safety and efficacy, and you can read that here:
I particularly like the fact that niacin can help lower Lipoprotein (a), which may be the single most dangerous particle in terms of plaque risk and one that does not respond to statin drugs.