The Dana 35 uses c clips to hold the axles in, the 44 does not. The 35 is a bit weaker, but with a super kit can be safe up to 35" tires (I wouldn't turn any higher than 33's on my 35). The D44 has a larger ring gear, and would be more suitable for a locker. The 35 can also be locked but requires a super kit.
My opinion. If you don't plan on anything larger than 33's you'll be okay, if you want bigger go with a 44.