Can you hide the vibrate() call behind an abstraction which you can replace depending on which platform you are using?
For example
var vibrateFunc = function(time_period) {
if (navigator.userAgent.toLowerCase().indexOf('chrome') > -1) {
console.log('vibrating for ' + time_period)
} else {
navigator.notification.vibrate(time_period)
}
}
and then have your app code call vibrateFunc() whenever it wants to vibrate.