I belive usual agarose G shuld do the work. When IP dosn't work with ubiquitinated proteins you shuld rather look what epitope is recognized by your antibody. It might be that during the ubiquitination process the active site of the protein might be lost. It is especially possible when recognized epitope is particualry large most of the protein. I suggest using antibody with short epitopes recognized at C or N terminus. 

Sorry, I should've specified. I meant what type meaning opinions on agarose vs magnetic, and what brands are best. In our lab we have switched to all magnetic beads, and recently gotten a large amount of the Pierce magnetic beads because they are supposed to be the most efficient. I have not worked with them yet myself, but I know that others in the lab are having big problems with their Co-IPs using the Pierce beads thus far

I have had good results with IPs using Invitrogen's Protein A or Protein G Dynabeads, which are magnetic. You just need to be sure that your antibody is recognized by Protein A or Protein G.