I saw one of your earlier questions was about Tough Mudder training. Do you still plan to do a race? Depending on your injury you will need to rehab your knee first and avoid any running for now (especially on uneven surfaces). Swimming is a great alternative and perhaps running/walking in the water will help with your cardio. Like Karin suggested, upper body ergometer could be an excellent alternative as well. Have you done any PT yet? Physical therapists can give you some great tips in getting your knee back in shape and work on any imbalances you might have. Muscle activation therapy can also be beneficial for you.
I hope this helps.