You can pipe stuff from eac3to to the Nero encoder.
Code:
eac3to input.data stdout.wav | neroaacenc -q 0.15 -he -ignorelength -if - -of output.mp4
Fill in paths were needed for eac3to, input, neroaacenc and output. The important thing is to have eac3to output to stdout and nero input from stdin (-if -). You also need -ignorelength IIRC.