We had trouble two years ago at splash and at dinasour (in hindsite a good thing!). My then 4yo dd was 40" barefoot so we assumed there would be no problem in sneakers. She hit the mark no problem at BTMR and LOVED it. Then she had to be measured a few times at Splash - be careful here as the ground is not level. She was short the first time so I calmly explained that she was just 40" at the doctors and at BTMR. The CM moved onto more level ground and DD again hit the mark. Be prepared to be measured at least twice every ride, its not a problem at boarding however as its level ground. It got to be a "badge of honor" for dd to have them "come at her with the stick" and then say "ok honey your all set".
I don't know what the deal was with dinasour as the measuring stick is permanent but she didn't even come close, different day same shoes! She did make it the next trip, about 6 mos later and liked the ride but I think it would have been to much for her anyway the first time. This trip she is just barely 44" and has been waiting patiently to be tall enough for space - could be the trip but we are prepared to wait if not.
If your son is 41" barefoot you should be fine, just be patient and make sure the CM is measuring on level ground and holding the stick level. Have a great time, fwiw - I would start with the barnstormer (if you haven't already done it), then BTMR and finally Splash Mountain.
TJ