By nature, cardiovascular exercises are going to be repetitive exercises. We're doing the same thing over and over and over again and this can really be damaging for our knees. It can create or accelerate the wear and tear process. Now some of your cardiovascular options are a little less strenuous, towards this wear and tear process.
By and large, if you're just looking for a straight answer, running is going to have the most problems or cause the most problems. Staying off of the floor and maybe doing biking, will create the least problems. But by and large, you can get by with running. You don't need to give it up all the way.
I think the smartest advice is to try to break up your week. Don't do the same cardiovascular equipment or exercise two or three days in a row. You might want to take a day off in between, or you might also, just might want to interval your training by doing a bike workout on a Monday, and then maybe a run on a Tuesday, then an elliptical trainer on a Wednesday, and then maybe start over again by Thursday or Friday. Rarely should you try to do the same thing two or three days in a row. That can accelerate the wear and tear process.
In general, if you're having trouble already, you're going to worry about running the most. That has got the most problems associated with it. You have your foot hitting the ground, so you have a lot of force going up your leg. It can cause a little bit of stress to the knee and eventually it can create some cracks and fissures in the cartilage. So running is the one you might want to be careful with.