I own a 1999 Sienna, bought used and missing the owners manual. I am trying to lower the spare tire. I see the cable which holds the tire up, running into a box mounted under the van, off to the side of the spare. Is there a tool or handle which lowers the tire?

If I remember right (never got a chance to lower the spare myself though), the tool to loose the tire nuts when you change tires is used for lowering spare tire.

to find where and how to lower the tire, lift up the carpet in trunk and there should be a little bolt to lower the tire

The problem is in finding the little hole in the carpet as there is no sign that the carpet is cut, so you must look careful to find it.