Yes, avoid the '99 to 01 Cherokees with the 0331 head.
When these heads crack, they are often replaced with heads from pre-'99 engines. If you find one so modified, it may be worth considering.
Otherwise, buy the best-condition Cherokee you can afford. Also, even though Cherokees have had the 4 liter engine and 4 speed Aisin auto trans since 1987, there were many detailed improvements made over the years. So, the newer the model, the better (up to '98, of course)