I'm not Durk, and didn't sleep at a Holiday Inn Express last night, but I did recently go through a similar experience...
You'll have to find the control box in any case. I just bought 2 generic ebay fobs and did this myself - my 98 only came with a valet key and 1 nearly-broken fob, so I had to get more.
If you just buy a fob, it won't have any effect on the car until it's sync'd with the box (there's a green button recessed in one side of the RS3000 box, and you have to press that and the fob's lock button simultaneously to sync them, so the fob will work on the car).
I found info while searching for mine (which WAS under the driver's seat, but I didn't recognize it)...
* Another user once found his ziptied below the steering column, but his post also shows other places to check:
http://www.toyota-4runner.org/3rd-gen-t4rs/141320-rs3000-vip-alarm-locations-98-sr5-help.html
* Someone else found his box under the carpet under the driver's seat:
http://www.toyota-4runner.org/3rd-gen-t4rs/74915-adding-remote-getting-ecu.html (that thread also links to ebay listings for the box so you can see what it looks like, in case there's a question about it).
In case you do find it, heads-up, there's multiple "sync" methods floating around. One has you turn on/off the key twice, then lock/unlock the doors 5x, etc... That never worked for me. Pressing the buttons at the same time did.
Good luck.