Stick your head under the dash and follow the noise to the beeper and unplug it.
I'm not certain if the Samurai's were fitted with them, and it may vary from one country to another, but my '93 Swift has a beeper under the dash, near the center, on the passenger side. It beeps if the driver's door is opened with the key in, engine off, or if the door is opened, lights on, key in, engine off - I'm guessing you have a wiring problem that may be causing yours to beep when it shouldn't.