First off where is the location of your pain? Is it the patella tendon (thats the tendon that connects the lower part of the patella/"knee cap" to your tibia) or is it at the quadriceps tendon (tendon that connects the quads to top portion of the patella)?
First off tendonitis is not any reason to sit out or stop training!!! Unless it is so severe that you cannot continue to train. If it's just a bit of soreness, then you can train or run through this. If the pain becomes sharp, shooting, or stabbing then stop!!
A lot of times people develop patella or quadriceps tendonitis because of tight hamstrings. This is because they are antagonist muscles and work in opposite directions. Hamstrings flex the knee and extend the hip. The quads work to extend the knee and the rectus femoris (one of the four quads) serves to flex the hip. So if you have really tight hamstrings, the quads have to work harder to extend the knee.
My recommendations would be to begin an aggressive stretching program for your legs and hips. Include piriformis, hamstrings, quads, hip flexors, gastrocnemius and soleus stretching. I would do dynamic stretches before activities and static stretches on your days off and following activities. On your days off when you are able to do static stretches, try to do them 3-4x's a day. Make sure you hold each static stretch for no less than 30 seconds and do each stretch at least 3-5 times for each muscle group.
You can continue with the ibuprofen if it seems to be helping. 1800 mg(3-200mg tablets 3x's/day) per day will give you pain relief but to get true anti-inflammatory effects you should take 3200mg per day (4-200mg tablets 4x's/day)
Some people will recommend open-kinetic chain exercises for tendonitis, but my philosophy is to never have athlete's perform knee extensions because of the shearing it causes at the patellofemoral joint. Also, it's not a functional exercise. Plus, tendonitis is an "overuse injury", so why would you do even more exercises for such an injury. I have have seen better results with my athletes just by having them do an aggressive stretching program.
Ice is great following activities. You can use an ice pack/bag for 15-20 minutes following training and stretching. You can also take paper cups and fill them with water and put them in the freezer. Use these by tearing off the top of the cup and then massage the area for 8-10 minutes following activity. If you do not have any swelling, you can use a heat pack or heating pad before training. NEVER USE HEAT AFTER TRAINING OR IF YOU HAVE ANY ACUTE OR NEW SWELLING!!!
You could also look at maybe purchasing some neoprene sleeves for you knees. These will help to keep the tendon's warm. If it is patella tendonitis, you could look into purchasing a "Fluk" knee straps. Many of the athlete's I have worked with have found these to be useful.