You really can't go wrong with either. If you're not sure about it and just want to give one a try, Tools of Destruction is cheaper. On the other hand, the graphics, effects, and such are slightly better in A Crack in Time (and I mean slightly, as Tools of Destruction looks awesome as well). Gameplay-wise, they're really similar, except that A Crack in Time gets rid of the somewhat kludgy and difficult to control 3D space flight sequences and replaces them with a more 2D model that's easier to control (it will make sense when you play it).
Story-wise, they form a bit of a trilogy (with the downloadable Quest For Booty in the middle), so if you're really looking to follow the plot, you might want to start with Tools of Destruction. That being said, the plot didn't really seem all that significant to me while I was playing.