Anything is possible, it pretty much boils down to how much money you have to spend and how mechanically inclined you are. The more you can do yourself the less it will cost you.
A Hemi would be cool, but it's probably going to be more expensive and you'll probably have to make your own motor and transmission mounts. Like others have said, it would be ideal to find a complete engine (with all computer controls), transmission, and transfer case drop out from a wrecked Ram 4x4 pickup. Then the main issue would be getting it all to fit in place. You'll have install a high pressure fuel line and electric fuel pump for the fuel injection. You could possibly use the radiator from the Ram if the Wagoneer one couldn't be made to work (I'm not familiar with the 5.7 Hemi and it's hose sizes and layout). If you have power steering, and you probably do, you'll have to adapt the metric power steering hoses from the Hemi engine to the english threaded Wagoneer power steering gear box (actually your 1988 might have a metric hose gear box, I don't know). I think you can find adapters for that if you need them. You'll need to modify your exhaust system to match up to the Hemi, as well as weld in oxygen sensor bungs. A complete new exhaust would be the way to go. You'll have to either convert your existing transmission shifter to the Hemi trans, or buy an aftermarket shifter. If the Hemi trans is a manual, you should be okay using the shifter with it. Aside from that you'll probably have to get your drive shafts modified or buy new custom ones.
A great place to look for the engine, transmission, transfer case set up is Ebay. A lot of car recyclers (junk yards) sell on there and some good deals can be found. For some reason though, engine and transmission packages are common but I've never seen the transfer case as part of the deal, they're usually available separately. Here are a couple of links to give you some idea.
http://www.ebay.com/itm/10-Charger-5-7L ... 0e&vxp=mtr
I don't have a clue as to what transmission the Charger came with so finding an adapter to mate it to a transfer case might be a major undertaking.
Seek and you shall find, I just said the transfer case isn't usually included, and boom, here's one that is.
http://www.ebay.com/itm/ram-1500-5-7-he ... 34&vxp=mtr
Instead of individual links here's the complete Ebay search.
http://www.ebay.com/sch/i.html?_from=R4 ... e&_sacat=0
Personally, being the owner of a J20 and the fact that Chrysler dropped the J series as soon as they took over the Jeep brand, I don't feel that much of a loyalty to them. Everything is readily available to swap a new GM LS engine into a FSJ fairly easily and there are tons of aftermarket parts available for them. I prefer the LS engine myself, but to each their own, and a Hemi would be cool. Good luck if you decide to do it.