My DD's Santa pictures at 18m and 2.5yo pictures were taken with me holding her, and both of us next to Santa.
This year, (3.5yo) she was completely comfortable sitting with him and getting her pic taken.
Honestly, if you want a good picture with just your son and Santa next year, you can try to the mall Santa first... But if he is not comfortable, I would look up a local photographer. A lot of times, they hold "mini sessions" with Santa, with special prices around Christmas. Your son will be less overwhelmed, and you will have a chance to let him see and get used to the giant, hairy, scary stranger dressed in really bright clothes, instead of being expected to be thrust onto his lap and expected to just take it calmly. (I would compare it to being suddenly pulled out of your car by a big, hairy stereotypical biker. Lol.) You will be in a more relaxed setting, and your pictures would be a higher quality.