DOnt get discouraged if he's only 3 mos. Lots of puppies that age just can't hold it all night long.
One other option for you is to get a BIG wire crate that will be large enough for him as an adult, and put his bed, etc in the rear of the crate, and a small potty area of newspapers in the front.
My middle pup could not make it through the night until she was about 15 weeks or so, and this really helped her. It did not hinder her housetraining at all.
And YES< I would have the crate INSIDE the room with you if you are going to use it. He may be asking out and you just don't hear him in the night.