It seems that the issue may be due to the iframe being obscured by another element that is intercepting mousewheel events, such as the canvas or a css3d div with trackball controls.
POTENTIAL SOLUTION 1
To address this, consider adding an invisible plane within the webgl scene that corresponds to the css3d object and listen for mousewheel events on the window instead. Upon detecting a mousewheel event, use a raycaster (refer to Mr. Doob's interactive objects examples) to determine if the invisible plane is being interacted with. Before adding the plane to the scene, associate the desired element to control as a property of the webgl plane that is intersected by the ray. This will facilitate easy retrieval of the element during intersection checks.
POTENTIAL SOLUTION 2
Alternatively, keep a reference point for the position of your iframe and calculate the distance to the iframe using THREE.Vector3().distanceTo(otherVector3). If the distance is sufficiently close, initiate scrolling for the iframe. Remember to continue monitoring mousewheel events on the window.
NOTE: It should be noted that this method enables partial interactivity for the iframe, specifically for captured events that can be triggered and passed along.
NOTE: Please be aware that scrolling cross-domain iframes is not supported...