I figured out that the '-size' option isn't part of the php thumbnailing method. Once I added it manually, the following php code actually ran slightly faster than the command line.
$image = new Gmagick();
$image->setSize(200,200); // This sets the size of the canvas. Should be roughly twice the dimensions of the desired thumbnail for antialiasing to work well.
$image->readImage('/tmp/large.jpg');
$image->thumbnailImage(0, 100);
$image->writeImage('/tmp/small.jpg');
This post helped quite a bit.