Bass Boxes are better if you have a bit more money to spend, bass tubes are the budget option. The difference between the two is that the bass box has to have a seperate amp, its usually more powerful and of a higher quality and it takes up more room (usually). The bass tube is what is known as an active subwoofer which means that the amp is actually in the tube, which means that you cannot be fussy over the components you choose, are usually a lot cheaper and are nowhere near as good.
Subs and amps are so cheap now that you are better off staying well clear of bass tubes.