Até onde eu sei, alguns Boeing 747-400s (BA, Air France) tinham lavatórios dentro do cockpit. Aparentemente, o Boeing 747-8 Intercontinental tem um lavatório atrás da porta da cabine :
... Lufthansa Boeing 747-8 Intercontinental is unique in that the flight deck crew have their own lavatory, ... behind the locked cockpit door, allowing for extra security and a non-disruptive cabin service involving trolleys blocking the door.