It's a close call between SGU and SGA for me.
SGU is the most recent, and therefore a lot about it is better than the previous series, but because of the more limited nature of what they do week to week, they're not as ambitious with their CG on average. But the brown aliens blew away any character work they've done on SGA and SG-1 by miles. They did a lot of moving camera shots with perfect camera match, and the aliens were so detailed with a lot of texture. The blue aliens didn't impress me as much.
A lot of SG-1 is aging, so a lot of the CG is looking quite bad now. The later stuff looks alright, but I think by that point they were probably putting more into SGA.
SGA has a lot of impressive CG, especially some of the water sequences. The pilot was great, Grace Under Pressue had some impressive underwater shots, The Eye had some amazing shots, and some of their week to week establishing shots of Atlantis just gorgeous.
So the best of SGU wins, but overall SGA did more impressive and ambitious work imo.