It's hard to get a sense of scale, but would something like this work? Not 100% happy with it but...

Red represents the wall space I assume your window treatments will take. Green is lamps/small tables/wastebasket/etc. Gray dots are the area that will have to stay clear to accomodate doors.

The bed is turned widthwise into the niche. Since the bed fit lengthwise, I'm assuming it will fit widthwise with room to spare, so your son can have a lamp or side table near the bed.

I would move the chest of drawers to the right of the window. This will stage that area is a dressing space (I like to arrange rooms in "zones"). Closet access isn't ideal, but it isn't blocked.

I would then add a bookshelf, wall shelves, etc. across. I'm not big on symmetry, but I am big on giving kids the things they need for a comfortable room and I think a bookshelf will be functional and still give you some places for decorative accents, art above, etc.

On the wall to the left of the entry, I would put a desk or other workspace. Especially if he has a computer. Here, too, the green dots represent a lamp and wastebasket.

You could place a large rug in the center of the room and keep it clear for a play space.

Anything else I could quickly come up with involves turning the bed so that it intersects the room (e.g. at some point you would have to walk around it) and you mentioned that's a pet peeve so I didn't entertain it as an option.