The AMC 20 found in CJ's has a terrible reputation. Downright dismal. I will sell you one for $40 and I have seen many for sale on CList for less than $100. $200 is a terribly inflated price. If you do go with the AMC20, you will have to buy one piece axles for it and also weld on new mounts.
The axle to get excited about is the Dana 44 from an early XJ or from a Commanche. The XJ Dana 44s are often worth more because they are a direct bolt in to XJs. In our case we need to weld on new perches and shock mounts anyway, so the best axle is actually the Commanche Axle. A Commanche axle has the perch on the underside and it doesn't have any shock mounts because the shock attaches to the Ubolt plate, very similar to the way an AMC Spirit axle is set up. The best thing about Commanche axles is that alot of them have factory limited slips because alot of Commanches are 2WD. The Commanche axles are also much more common. I purchased two of them so far for $300 without limited slip and $350 for limited slip.
If you have a stock AMC 360 and are still using the stock Motorcraft 2150 carb you realistically have the same power and torque as a 4.0. Its very humble. If so you don't need anything fancy. A Jeep XJ 8.25, Dana35, or Ford 8.8 are all more than enough for that engine. The Dana44 is only marginally better. I really only get excited about them because of how easy it is to adapt rear calipers to them and because I never want another wheel to fall off. My family has been driving Eagles for a long time. We've had a rear wheel fall off three times.
For my big budget AMC 401 powered SX4, I will be using a custom Dana 60 with Warn full floating axle conversion and 5x5.5 bolt pattern. This is something to consider if you heavily modify your 360 to its full potential in the future. Its realistically possible to double the power and torque from the factory values if you're willing to put the time and money into it. A Dana60 with the 5x5.5 bolt pattern is found factory installed under Jeep trucks, but those have a flanged axle. The idea behind a full floating axle is that you can shear the axle and your wheel won't fall off. That is also the huge advantage of the Dana 44 over the Dana 35. The axle is also less likely to break since it no longer has any vertical load on it. The weight of the vehicle is also supported by the axle when you have a flanged axle. A full floating Dana60 is only found with 6 or 8 lugs from the factory, but Warn offers a kit to convert one. If I go with a fully assembled, converted, machined and lightened, professionally produced Dana 60 shortened to my liking I expect to spend between $5000 and $6000 dollars.
There was a thread on here about the minor machine work needed to install XJ wheel bearings into the stock Eagle Independent Front Suspension. That same concept also works to convert the front of an Eagle to 5x5.5. That is a way to keep the same rims front and back after upgrading the rear axle.