You Tube 3D format is SBS. Any downloader plugin for YT player for 2D will work for 3D. Most use MP4 You could convert the SBS to TB but that would be kind of counter productive for best resolution of the image as the horizontal is already reduced with the SBS format.
My 3D videos and more
Don Landis HT System: Projector Sony VPL VW665ES Players: Samsung UBD K8500 OPPO BD93 Sony BDP S6200 All Regions Player Denon AVR 4311ci, 7.1 JBL Professional series and Klipsch PS3, XBOX360, Dish VIP722K; 3D Edit Suite: Edius7.53, Vegas Pro v13, Power Director15, i7-950, LG 3D TV DM2752
If I understand right and you have just a download problem, I use 4k video downloader free (www.4kdownload.com), selecting original quality in settings. Unless you are trying to convert those videos or else.