The most frequently mentioned aftermarket heater core for the pre-03 TJ is probably Spectra. I am not familiar with some of the other brands but a google search of the discontinued Mopar part number for your year should yield the available alternatives. You can also do a part number cross-reference search on many auto parts sites.
There will probably be someone who feels the urge to opine that anything other than genuine Mopar is inherently junk. I'm not sure that Spectra should automatically be placed in the junk category, but I don't know where Spectra fits in the hierarchy of available options. I have inquired with a number of repair shops in my area and also my local parts house about Spectra heater core warranty claims. The response has thus far been no more or less than any other brand, including manufacturer brands. That doesn't translate to Spectra being as good as Mopar, just that locally at least no one in the business seems to think Spectra is any worse.
I can still buy a Mopar branded Valeo heater core for my '06 but the price is $224. I can buy the Spectra version for less than $50. Although I am tempted to save $175 by going Spectra, the shop time for the job is 6.5 hours and although I may be retired, 6.5 hours of my time (more realistically 8+) is still worth a lot more than $175. It isn't worth the gamble that I might get a lesser quality part by trying to save a few dollars. You guys with the early TJ's don't get to make that choice, the only heater cores available for you are the cheaper aftermarket versions.
I think the prudent course of action no matter what brand of heater core is purchased, including Mopar, would be to have it pressure tested at a radiator shop prior to installation. There is too much installation labor involved not to ensure in advance that it is a good part.