Well, I like the Dana 44 better. There are different flavors of 8.8" Fords. The 28 Spline versions aren't much better then the stock Dana 35c. Then there are the better 31 spline which are the one's to get. The axle tubes are thick, around 3", and the shafts are 1.31" diameter. In comparason the Dana 44's tubes range from 2 3/4" to 2 7/8". Generally rear axles used smaller diameter tubes then the front. The 8.8" from later Explorers come with disc brakes and up to 4.10 gears. I should also note that they have C-clips, prone to having the tubes spin and bearing caps loosening up. That's why many use those pre-load diff covers.
I like the D44 since I plan on replacing my front axle with a Dana 44. Then I'll be able to interchange gears and lockers. Dana 44's are probably the most widely produced axle. The only down side to the XJ Dana 44 is the cost. But at $225, it's a good price. I think you can use the Dana 35 brakes or go with ZJ D35 Disc's.
I don't think you'll find a 8.8" for under $300. Most want $500-900. The biggest advantage of the XJ Dana 44 and Explorer 8.8" is that they are 5 on 4.5" bolt pattern. Meaning you won't need to swap the front axle right away. If you got a Scout axle, then you'd have to consider getting the axle's and drums redrilled to 5 on 4.5" or else swap out the front axle at the same time.
Here's a article on how to swap a YJ and some info on the XJ Dana 44
. Getting brackets for a TJ would be the most expensive part I think.