This usually happens everytime we pull from upstream a new version.
Hope that this can be resolved once and for all this time.
It works if you pass -stdlib=libc++ to clang++ while compiling and linking.
Pushed a fix to bsnes repo. Makes clang -stdlib=libc++ default compiler for OSX.
Building from libretro-super is still broken because compiler="$CXX" is passed to make, short circuiting the ifeq ($(compiler),) block of the Makefile.