I have a 94 4x4 3.9 with a 5spd manual trans. When I accelerate i can sometimes hear what sounds like a rattling noise(sounds almost like a chain being dragged on the ground). The noise comes from the back of the truck so I'm guessing it has something to do with the rear axle, what could it be? A bad bearing or something?

It could be anything. If you sure it is the rear it may be the gears or a bad bearing and you got low oil. Or bad brakes. Or bad U-Joints.

The best thing to do is first go under the truck and take a look. Push and pull things. Lift up the rear and spin tires ect.