Joint pain can be an EIM(extra intestinal manifestation) of crohns disease and UC. Some EIMs run concurrently with active IBD while others run independently. Although it is a good idea to let you GI know about the joint pain it is probably something you should see a rheumatologist about as well.
My son has CD and has peripheral arthritis that run concurrently with his active flares, this affects his knees mostly but also feet/ankles and hands, this occurs when his CD is flaring.
He also has spondylitis or spondylarthropathy which can occur with IBD, it runs independently of his CD and affects his lower back and hips. It was dx'rd by his rheumatologist and even though his GI was aware of his pain he isn't in a position to dx spondylitis or does he oversee that treatment, which is needed since this dx can cause joint fusion.
An appointment with a rheumatologist is probably a good idea and finding one familiar with IBD is also important.
I hope you get some answers soon.