The 44 is a more desirable axle. Maybe not to you, but in general. They ARE getting hard to find, and generally pull really good money. Even if you're not going to use it you should go get that one from the junkyard. You should be able to make at least $100 off of it just by pulling it and reselling. I've seen several in the $4-500 range recently.
I was planning on putting an 8.8 in my MJ, mainly because it's a good axle that's cheap and plentiful. I grabbed one out of the junkyard and had it sitting here ready to go in when I had a good deal on a 44 come along. I jumped at it, and it'll be going in soon. The 8.8 will be going up for sale.