NaCl gets a lot more attention these days, but I'm convinced both are fine. On the one hand, NaCl is pretty hardcore DJB-ware (poly1305-aes, salsa20...), and normally I'd err on the side of conservatism. OTOH, it's also really really good DJB-ware, so I can't blame anyone for using it :)
I personally prefer sodium's Python versions. Whether to deliver libraries in the Python packages or to use shared libs remains an open problem: I am somewhat convinced the former's better, but I can certainly see the cases where it'd go wrong.