Hi Aaron! I've also had crohn's for a few years now (since 2002) and within the last year my joint pain has increased substantially. I've always had sore sacroiliac joints with hip pain, but this past year the pain feels like it's everywhere! I've had the SI joint pain, hip pain, and also pain to my fingers, wrists, elbows, shoulders, knees, ankles and toes. It's hard to live life some days because of it. My MRIs are always negative for inflammation (to my back at least), which is good, but also very aggravating. It has been found that I have severe hyperflexibility which definitely contributes to the pain, but they think that a lot of it is crohn's related arthralgias. Since I cannot take any NSAIDS, I take hydrocodone. It's not ideal, but it helps a lot. I've been on it for many years and take it responsibly. If that's something you have to do, be careful with it because it's very addictive (as I'm sure you know!!). I also use topical Voltaren gel which actually works quite well. This might be an option for you? I'm going to start physical therapy tomorrow to see if I can strengthen the muscles around the affected joints-- hopefully this will get me back into pilates! Right now the pain is way too severe to even think about working out.
I know I didn't give much advice, but know that you're not alone with this one. I would say that my joint pain is the worst part of my disease...and it seems to be the hardest part to control. Good luck to you!