Where is he pointing? His thigh? Where his leg meets his torso? Groin pain can come from the hip joint. Pain on the outside of his hip or his thigh is more likely to be muscular. Try and get him to point to where the pain is.
There are extra-intestinal manifestations of Crohn's. It can affect the joints. You can have arthralgia, which is joint pain. It hurts, but it's benign and goes away once the Crohn's is under control.
Or you can have arthritis which is inflammation in the joint, which causes pain. The inflammation in the joint(s) may go away when the Crohn's is under control - that's more common when large joints like hips or knees are involved. Or the inflammation in the joints can be separate from the inflammation in the gut, like in my daughter's case. In her case, her Crohn's can be in remission and she will still have active arthritis or vice versa.
The GOOD news is that both MTX and Remicade do treat arthritis, so even if he has that (which he probably doesn't), he will likely get better as the drugs kick in.
When (what time of day) is his pain worst? What makes it worse or better? Does heat help? Does moving around help? Does he look stiff or walk stiffly, particularly in the morning?
If the pain persists, I'd ask to see a pediatric rheumatologist. If it goes away, I'd just wait and keep an eye on it.
In terms of helping with the pain, a bath is a great idea! You can also use heating pads or ice, depending on his preference.
I agree with what other parents have said about MTX and antibiotics. The dose of MTX he is on is teeny tiny - those warnings are generally aimed at people who are using MTX as chemotherapy and are taking 1000 mg or more - not 10 mg. The pharmacist will often flag the script for abx, but your GI has been using these drugs for years and would not prescribe something unsafe. My daughter has been on Amoxicillin plenty of times with MTX - no issues. You did the right thing - you checked with your doctors and they aren't worried, so you shouldn't be.