Hi Kelli
It sounds like you will need a good manual (hands on) physiotherapist with rehab skills who can give you advice regarding a progressive eccentric loading programme of the knee to improve your tendon strength, whereby settling your patellar tendon pain.
Mobilisation of the patella may prove beneficial also as this can often become stiff, and glute/quads strengthening combined with proprioceptive (balance) rehab will also round out the program.
They should also be able to help you out with alternative gym/cardio options so you can begin to regain your fitness without compromising your knee symptoms. All the best. Mike