The stock TJ sub runs at 1ohm, so there is no direct replacement. Having said that, if you just pickup any cheap 6.5 inch sub and put it in there it'll sound much better than a blown stock one. Since the stock amp is setup to run at 1-ohm, though very low power, your 4-ohm sub will work, but it will just be underpowered.
So, if you're going to reuse the stock amp, get a very cheap sub and go for it.
If you want good sound from a replacement sub, you'll need to disable the stock amp and use an aftermarket one.