I would suggest it's to do with the new arrival and his developmental age. I know with my 2yo, he is eager to show me everything he knows words for, stuff he can do now etc and if I had a little one, he'd probably be frustrated that he didn't have all my attention for it and resort to the only other way he developmentally knows how to be comforted, and that would be to cry. It's not manipulative in the sense adults think of it, it's just all he knows to do to get you to notice where he's at. That's what we all want from those closest to us, isn't it? Just some validation? It will come and go, and will probably 'go' more if he's more physically included in things - like letting him go to sleep at night in your bed and stay there for a little while. He'll get over the cramped conditions and get back to him bed soon enough, surely. Even if he doesn't and you need to force the issue a bit later, at least he will feel a bit more secure about it.
I sense that it's his sense of security and sense of 'place' in the family that has been interrupted. After all, your DD is also coming into a transitional time of 12 weeks and of your attention is a bit tied up!
There's not enough information in your post for me to see if you have been involving him in the day to day care of DD. I would suggest to do this (get him to take rolled up nappies to the washing machine, pick out some clothes for her to wear, cuddle her while mummy goes to the pantry etc, instead of asking him to wait and be patient (they can't do this very well at 2!).
Anyway, I hope I haven't told you how to suck eggs - just my first impressions from your post.
It must be so hard to have to split your attentions between two kids who both need different types of attention!