I am unsure if there is a currently maintained version of FUNWAVE with NetCDF output. There is an HDF5 output branch, however, has not been kept up-to-date with the current version of FUNWAVE. The current ASCII output is a bit slow since it does not implement parallel writing. The raw binary output does implement parallel writing and can speed up the runtime, especially if you are outputting at a fine time resolution. I hopefully solved the issue you posted previously with reading the binary output, if not we can talk about it more in that thread.
Mike