How can I rotate a mesh by 90 degrees in ThreeJS?

The threejs rotation uses Radians (as you might know)

you can use this

mesh.rotation.x = Math.PI / 2;

or

mesh.rotation.set(new THREE.Vector3( 0, 0, Math.PI / 2));

You can rotate an object by using this function:

function rotateObject(object, degreeX=0, degreeY=0, degreeZ=0) {
   object.rotateX(THREE.Math.degToRad(degreeX));
   object.rotateY(THREE.Math.degToRad(degreeY));
   object.rotateZ(THREE.Math.degToRad(degreeZ));
}

// usage:
rotateObject(myPlane, 40, 30, 20);

Let's say meshToRotate needs to be rotated by 90 degrees in X axis. Then do the following.

var meshToRotate = new THREE.Mesh( geometry, material );

//Rotating mesh by 90 degree in X axis.     
meshToRotate.rotateX( Math.PI / 2 );

Tested on r96, you can also use

mesh.rotation.setFromVector3(new THREE.Vector3( Math.PI / 2, 0, 0));