J.H.
I have a 6 yo son and 3.5 yo daughter. They have been sharing a room for over a year now and it has always been fine. Instead of the bunkbed route, we bought 2 junior size loft beds. Each one is only about 4 and a half feet off the ground, so we maximized floor usage, and each child has their own space under their bed. My 3 yo hasn't been a napper for quite awhile, but on off/rough days when we do need more than quiet time, I will put my son in our room to lay down. Also, they go to bed at the same time at night, and we have become very insistent that they do not bother one another in the morning. My son can be quite the morning person while dd can be quite the "crank" :-) I would consider the lofts over the bunks, and also, I would echo a previous idea of considering trying to adjust your son to 1 nap a day. I don't know if sharing a room has done the trick, but if it's any encouragement, my children get along great most of the time, they have learned great teamwork in keeping their room cleaned up when we ask, and they have become pretty good at sharing and taking turns, and I think it's because they spend so much time together. Good Luck!!