I have stayed at Pavillion de la Reine, but not Relais Christine. I thought Pavillion de la Reine was an excellent hotel, although it is typically Parisian--small rooms, etc. But I thought the service was good and the location on the Place des Vosges was very good.
While I haven't stayed at Relais Christine, my wife and I are very familiar with the area and have longingly looked through the courtyard and into its lobby. In general we prefer its Left Bank neighborhood to le Marias when Relais Christine is located. That said, Relais Christine is an a more touristy area--it appeals to us (probably since we're tourists), but I suppose more seasoned Franco-philes might scoff.
Not sure if this is helpful--I know one property is nice and suspect the other is as well.