Well, we're going to be taking Renko/Sumireko/Chen with us anywhere, so it's not like Yukari appearing will leave them stranded somewhere else. Unless you wanted Koishi there too for some reason.
I think we should do Koishi first just because she's not exactly part of our "party". She's got less reason to just tag around with us, and she might not want to just sit around at Eientei and wait for us to come pick her up either. Sumireko isn't really a time sensitive matter now that we solved the big issues, she can wait ten minutes.