The very last train from Tokyo (Keisei Ueno Station) to Narita Station is a local service train at 11:24pm (11:28pm Nippori Station) arriving in Narita (Keisei Station) at 12:55am.

However if you find yourself in Shinjuku at around 10:30pm, you better start leaving out to Ueno or Nippori to make the transfer on time earlier or later if you aren't too familiar with the train system and transfer tickets.