It looks like Anaconda no longer installs the mpl_toolkits module (which installs mplot3d) by default when you install matplotlib, at least on on some systems.
I just ran into this problem on Windows: I had to do using Conda; Conda.add("basemap") to install mpl_toolkits, which forced a downgrade of the numpy package.
Probably PyPlot should be updated to work (with 3d plotting disabled) if mplot3d is not available.