It depends when you are planning on coming in and hour of the City.

I echo the recommendations to take the Lakeshore West line which has regular service and runs no less than every 30 minutes and as frequently as every 10 minutes.

If you're going to be catching the train before 8:00am then pick Aldershot or Burlington GO Stations.

If you're catching the train a bit later then drive to Oakville GO Station and use the parking garage. The traffic chaos around Burloak Road will likely have dispersed by then and it will be a faster ride on the "milk run" which stops at all stations.

In either event you'll be able to skip the cluster**** they've created on the Gardiner Expressway and Lakeshore (look to the right out the window as you come into the city and you'll see the mess you're skipping).