M.S.
First off, I would like to say that my daughter slept with us until her 4th birthday. We only got her out because she picked out a great new bed for her birthday (with a slide on it) and she chose to move so we could have a baby for her (or so she thought). She wanted a baby, and I told her there was not enough room for 4 people in my bed, so we couldn't have more kids until she was sleeping in her own room.
Try sleeping in his room for a couple nights, then stay with him while he falls asleep for a few nights, and then after that explain to him that he is a big boy now and needs to sleep in his big boy bed like everyone else. The hard part is that he is old enough to understand that you don't have to sleep alone... you get to sleep with Daddy. So he will think it isn't fair he has to sleep alone. Is there an older sibling he can share a room with (just for sleeping)? After so long sleeping with you, the thought of being alone in the middle of the night is terrifying. Most adults even have trouble sleeping alone while a spouse is out of town.
If nothing works, then yes, the cry it out method also works with 3 year olds... just be prepared for manipulation, guilt, and tantrums. It will pass.