I am wondering if it is easier to swap in a 350 crate engine or find a V8 engine from a Grand Cherokee  to swap into a 1994 Jeep Cherokee.  

the jeep one will bolt up to your tranny and the chevy you will need an adapter but if you go with a chevy carburated you wont need to worry about the computer problems or just put in a carburated jeep v8 304 or 360 from an old cj and get passed the computer and tranny bolt up problems.  

How about if I want to to use a 5.2 or 5.9 from a late-model Grand Cherokee and swap out the computer?  

That's the ticket, get the new computer, too. Heck, if you get lucky find a wrecked one and buy the whole thing and take what you need and sell the rest.  Check out a Service manual or Haynes manual for wiring information, some of your wiring may be the same, or you may need to get as much of the new wiring harness as you can. Honestly wiring up the computer will be the hardest part, but you should still be money and time ahead over the cost of swapping a Chevy 350 plus tranny adapter plus fuel system (carb v/s fuel injection) since the Jeep V8 should bolt up to your current tranny.

Good Luck