Init app ondeviceready or load if it's a phonegap app or not. From https://github.com/triceam/PhoneGap-Legends/blob/master/js/index.js

pginit.js

//detect if web or phonegap ( via http://stackoverflow.com/questions/8068052/phonegap-detect-if-running-on-desktop-browser)
function isPhoneGap() {
    return ((cordova || PhoneGap || phonegap)
        && /^file:\/{3}[^\/]/i.test(window.location.href)
        && /ios|iphone|ipod|ipad|android/i.test(navigator.userAgent)) ||
        window.tinyHippos; //this is to cover phonegap emulator
}

function init(event) {
    console.log("init app");
}

if ( isPhoneGap() ) {
    document.addEventListener( "deviceready", init );
} else {
    window.addEventListener( "load", init );
}