Well first off, this should be posted in the Audio forum. But your new, so all's forgiven
You have two options:
1) Buy a new sub from Toyota which will be an exact match and maybe even be covered by your warrenty. No worries there. Just pricey.
2)Buy an after market one. This depends on what kind of setup you have.
a) If you have a powered sub (normally a small tube, or looks like a normal speaker), then that can be replaced with anything. It mearly wires into the normal speaker wires. For this, I would suggest a Kenwood powered sub. They make a compact one that sounds great, and is only about 2" high. Very reasonable on the wallet too.
b)You have a normal sub (which uses an amp), but it runs off a small factory amp(Looks like any other sub, probably a 8" or 10" sub in a box). Most likely it is this one. In that case, you can either get it buy a new one direct from Toyota, in which they would install it, or go aftermarket.
For aftermarket, you would have to find one that doesn't require much power. The best thing to do would be to check your manual and find out what the current sub is running for power. Then you could find something that would meet those requirements. Depending on the factory amp, that may be hard.