It's quite simple. In your extensions manifest to specify the icons as follows:
{
"id": "hub",
"type": "ms.vss-web.hub",
"targets": [
"ms.vss-work-web.work-hub-group"
],
"properties": {
"name": "Hub",
"description": "Something",
"uri": "pages/Hub.html",
"icon": {
"light": "img/hub-light.png",
"dark": "img/hub-dark.png"
}
}
}
Hope this helps.