It is most typically a black box under the driver's seat. You can buy remotes for it
off of eBay. Be careful that you buy the correct remote. If I recall, the black remotes work but some of the gray do not. Do a search for the FCC ID. The FCC ID for my remote is BAB237131-022
Here's
a thread that describes how to program the locks. If you don't have the box under the seat you could try the steps to see if the vehicle reacts.
Here is the factory alarm display:
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2004 4Runner SR5 SR5 - V6, 4X4, Moonroof , JBL, Leather, Stratosphere Mica
Installed Mods:
Spoiler,
HIR bulbs,
Kenwood DNX6960 Nav,
Back Window Up with Remote Mod, Rear Camera, LED Tails,
Key Reminder Disable, OEM Automatic Headlights,
Rear USB Ports,
Seat Heaters,
Aftermarket Third Row,
Heated Side View Mirror
Locations: VA