My well behaved cat and boxes!!!!!

It sounds to me like he is just trying to entice you into playing with him. It is more than likely more play than it is aggression. Very normal. I don't know how many times my cats have gotten into their "crazy moods" and swatted me while I walked by them, and usually they are "hiding" or in mid-play, trying to get my attention.

That sounds like perfectly normal behavior.  Try getting a toy on a wand and dangling it in front of the box for him to "attack".

This sort of reminds me of my cat with her scratching post. Sometimes I would scratch it a bit and it would entice her to run over and put all four legs around it and start scratching it as if she is saying "mine mine mine!!" It's funny to watch. And if I were to scratch another area, she would jump to that part and do the same thing, so I think it's just playing. 

Cats and boxes...yeah cats have powerful imagenations.

Homemade toys are the best.

Don't worry, this is normal as far as my experience. My cats will hide behind the couch, and then kind of "pounce" at me when I walk by, it's instinctual. Boxes are my cats' favorite, to sleep in, also to "hide" in. It's not about territory, it's about being sneaky (which cats like to do). If it's a problem for you, get rid of the boxes. My cats love boxes, so what I would do is encourage their "cat and mouse" game. Take a toy such as a wand with feathers or what not, and, when they're in the box, wave it in view and then out of view of the box. They love it. They may swipe at you as you walk by, but it's playful.