Ellipticals are a fine alternative, so are Recumant bikes or even swimming. Do that until your knees feel better then consider running again. You can run on sand, that is easy on the knees, or you can get a treadmill with a little more give. Nordic Track has some treadmills with what they call reflex deck, it what I recomend for customers with bad knees.

The elliptical is great because you are actually toning and getting a cardio workout at the same time depending on the resistance which can be adjusted. You can also WALK at an incline on the treadmill to tone your legs. Not sure of your weight but that may be why your knees hurt also if you just jumped right in your body is not used to the stress of running. Gradually with anything is the best. Good luck

The elliptical is easier on your knees, you could also try swimming. Swimming causes the physical stress you need without the joint damage.