The main thing you have to be careful of is over use. You can develop tendonitis fairly quickly returning to snowboarding because your tendons and ligaments aren't conditioned for this type of use. After suffering a broken foot and a knee contusion in consecutive seasons I returned too aggressively the following season and ended up having severe pain in a similar spot to what you are describing.
A few different things have helped. First, I'd recommend easing back into it. If you start to experience pain, stop immediately. I really can't stress that enough. Too many times I've just continued to ride with pain, only to have them develop ligament strain and tendonitis. I ended up having iliotibial band syndrome that took months of therapy, and rest, which I still didn't fully adhere to. If you have pain, stop, ice it to reduce swelling and jumpstart the healing process.
I've also reduced my angles from 18/-15 to 12/-9, which seems to help a bit. It takes the strain off my knees from being in a twisted position. I tend to keep my shoulders a little more square as well so I'm not opening up so much and putting so much stress on my back knee.
I think it also helps to get a binding that has good dampening and some canting. After trying a few bindings with canting I wasn't really sold on them because during back to back rides, I couldn't tell any immediate difference in performance, but since I've been riding them full time I've noticed my knees have had much less pain and stiffness after longer days on the hill. With the increased dampening, canting, and reduced angles I've definitely noticed an improvement. My knees don't develop that sprained-like feeling I've had to ride with in the past.
I also ice my knees regularly. If I've had a heavy day on the hill, and I start to feel some over use, I'll take ibuprofen to reduce inflamation and ice 2 times, once when I get home and again before bed. It helps my knees heal from any micro-trauma to the tendons and ligaments and helps reduce recovery time so I'm fresher the next time I hit the hill.
Another thing I've noticed is that some boots, particularly stiffer ones tend to contribute to knee pain, likely due to the angle they set your leg at. I've found a few boots that I just couldn't ride because they caused so much leg pain.
Hope that helps. Keep trying different things and eventually you'll figure out the right set up and recovery routine.