Long overdue, but I hope this helps others. I don't think there is a "best method". I always use the Qubit HS DNA kit using 5 ul sample of a 40 ul ChIP elution. This quantifies the DNA on the lower end, but it is quite accurate. Normally the Bioanalyzer gives a similar reading, at least within the Qubit range. It might be necessary however to create the standard curve with gDNA from your organism for the Qubit reading, as sometimes the lambda standards may differ in GC content.

Nanodrop is the least reliable, especially for very low amounts of ChIP DNA - usually impossible to quantify. I always want to know how people quantify their chromatin in pulications, because depending on the method of quantification they could be adding 10 ug or 2 ug of chromatin to their samples depending on the quantification method (Qubit normally gives values much lower than the Nanodrop).