Both have their advantages, and disadvantages. When choosing one you should look at the quality of the instruction. A good instructor will help you reach you're full potential.
That said I am a karate practitioner, and I highly recommend it for self defense purposes. Karate has a lot of depth to it, and there is so much to learn. Karate was created for self defense, and its a very good art to learn.
If your goal is to get in shape then I would recommend kickboxing because it typically focuses more on cardio then karate does. The training methods utilized in kickboxing are very aerobic, and will burn the calories.
That's not to say Karate cant be a good workout, because Karate can get you in shape too. I just give the slight advantage to kickboxing for a cardio workout.
You should visit the schools in your area and see which one you like best.