data.coord won't give you [ 'lon', 'lat' ] array, rather it would give you { "lon": 159,"lat": 35 } object.
You can get their values just like you would get value of any object like: data.coord.lat and data.coord.lon
So something like
var latitude = data.coord.lat;
var longitude = data.coord.lon
EDIT:
Similarly, for weather you can access weather using data.weather, however thing to note is that weather is an array. So, you can get hold of 1st element using index=0.
Effectively, you'll write, var myWeatherObject = data.weather[0]; //0 is index of 1st element
Again, to access individual weather properties, you can use:
myWeatherObject.id, myWeatherObject.main, myWeatherObject.description and myWeatherObject.icon