Hi L.,
We recently had the same exact problem with our 16 month old grand daughter whom we are raising.
She has asthma, and got bronchitis and for weeks was having difficulty sleeping. Instead of a swing she was sleeping with my husband and I and we would prop her up between us with pillows, and then have her nebulizer handy if her breathing got too strained. Once she was well, we had a heck of a time getting her to sleep in her bed. We started by laying with her until she fell asleep, giving her a large pillow to sleep on, then would leave her once she fell asleep, she'd wake up minutes after we got out of her bed. so instead of laying with her, which you couldn't do anyway with a crib, we then sat next to the bed rubbing her chest. Then it went to getting up a couple of times during the night to back to sleeping through the night and us being able to just lay her in bed at bedtime. It's all back to normal now, but it took 3 weeks after patiently working her through the routine change until she felt secure again. For her, and maybe for your son, its that fear of not being able to breath and choking....having us there close until she begin to feel secure again made all the difference.
Hope this helps.