Samurai axles, in stock form are maxed out at 33's.  The common problem that they have while running bigger tires are busted Birfeild's and bent axle housing.  You can add a truss to the axle housing and add trail toughs "double tough" Birfeild's. The double toughs are rated up to a 35" tire.  A some what good thing about a samurai axle is the size of it.  A Samurai on 33's has the same amount of axle clearance as Toyota does on 35's.
You are limited on locker selection with a samurai axle.  I'm pretty sure your choices are lock rites and quick locks, which in my book are not the greatest. Theres also mini spools that you can get also.

Toyota axles are a huge improvement!  There is tons of after market support for them, you have a wide variety of lockers and other goodies. The year range you are looking for is 79-85.  84 to 85 are the more desirable of the years, they have a longer lower truss which strengthens the axle up.
A stock Toyota axle is good up to a 35, then your pushing the limits of it.  You can do the same as you would with a samurai axle and get new berfeild's, which will get you up to a 38-39" tire.
Theres 3 sock gear ratios that Toyota came out with.  4.30, 4.11 and 4.10.  Its a nice little upgrade compared to the stock 3.73 that samurai's come with.
You have quite a selection of auto lockers and spools for Toyota axles.  As far as selectable lockers go, there is ARB and Toyota E-lockers. Both are not cheap, but well worth it especially if your going to be doing a fair amount of road driving.
One thing you will run into while swapping in Toyota axles is, samurais come stock with an offset rear axle.  Stock Toyota axles are centered, you can get a custom one made, or do it yourself.  People do run centered axles on samurai's, but you can run into  drive line vibrations from that.  People say to use a single cardan drive shaft to keep away from the vibrations.

You should have no problems with a lift when swapping to Toyota axles.  You just have to move the perches in a bit to line up with the samurai spring position.  There are tons of kits that will allow you to run Toyota or samurai axles.

Hope this helps out.

Amilla

Amilla has it about right, but you can also get an ARB for the Samurai axles and Trail Tough now has Chromoly axles for the rear as well. 

I like the stock axles myself, but if I was going to go bit I would swap over to Toyota.  Of course, now that I have enough money in my SJ axles it's not worth swapping over.