A great source for organic baby clothes is Kate Quinn Organics. Not only are their pieces high quality, earth friendly and super soft, but the textiles are beautiful. Some of my favorite items of Vi’s are from them because they are so cozy, practical and lovely!
Three stores in the city that sell their baby clothes are Natural Resources & Speesees in the Mission (a block away from each other on Valencia), and Mabuhay Kids in Noe Valley. They also sell clothes for older kids as well as bath & bedding pieces. I recommend their two piece pajama sets-they are insanely soft and will fit for longer than onesies-and make great gifts!
(TIP: Though prices are a bit steep for baby clothes, their online store often has great sales.)