Well everyone, you have helped me tremendously with my decision.  I'm going to go with the larger apt with the den.  Thanks to you guys now I know I'm not making a silly decision.  As much as I love the new apartment, and can't wait to move, I'm more excited for JoJo to have all that extra space and his own room!
 
Here's a pic of the floor plan with the den...I decided on the second floor with the cathedral ceilings.