You don't modulate the neutrino beam itself, but you could modulate the pion production beam. For typical neutrino beam experiments this is done with a large magnetic horn which focuses/defocuses (+/-) charged pions which then decay to (anti)neutrinos and (anti)leptons. By changing the current in the horn you could modulate the intensity of the beam to send data.

Needless to say this is woefully impractical, would require an extremely large neutrino flux and detector, and would have an absolutely abysmal bit-rate. Not to mention you'd likely only be able to send messages in one direction. But it could be done.

see: https://www.fnal.gov/pub/today/archive/archive_2014/today14-...