Congratulations on your new baby. I wonder if your son is still in the process of acclimating his senses from the peace and quiet and predictability of the womb to hustle and bustle of the real world around him. There was a book that was out about 10 years ago called The Baby Whisperer by Tracey Hogg. In it, she talked about several different baby personality types including one that was more sensitive than the other types. For this type of baby, she recommended:
Picking up your baby as gently as possible and doing it in very slow, fluid motion so the baby doesn't feel too startled or off balance.
Before you go to pick up your baby, talk to him in a calm, soft voice, and explain to him what you are going to do so that it is not such a shock when all of a sudden he is being picked up. (I think, even though your child is not going to understand what you are saying, he will eventually connect that you are talking to him this way so that means he's going to be picked up soon and, with this knowledge, he'll be less apprehensive.)
Making sure that the overhead lights are not to bright so that they are not hurting his eyes as he is being lifted up closer to them.
And -- I think she said this but am not sure -- making sure that Mom, Dad or anyone who is picking the baby up is not wearing any scented perfumes, lotions, etc. If The Baby Whisper didn't mention the "no scents" suggesion, I am since anything perfumey that you can't smell and he can't smell at arm's length, may be way too overwhelming for him once he is drawn closer to that person.
I'm not sure if this book is still available in the bookstores but, if not and if you would like to purchase it, I would try looking for it on e-bay. It does have a lot of great tips on creating a schedule, feeding, napping, sleeping through the night, teething, etc.
I wish you all the best for you and your new baby.