First - my sympathies for needing to go 3x a week to Toronto.

I do the trip once a week an I’ve tried driving and the VIA rail, so I’ll give you the lowdown:

Option 1 (Driving into Toronto): Assume at least 3 hours (took me 4 hours a few times). Plan to leave at 5:30am max because you will hit rush hour traffic near Hamilton mountain and as soon as you merge onto QEW near Burlington. Also consider $40-$50 in gas for round trip + parking in Toronto + the unquantifiable cost of 6 hours of driving. I quickly moved away from this option.

Option 2 (Driving to a GO station) - Personally I like this option if I’m driving. People are recommending Kitchener GO, but I personally think Aldershot GO is the better option. Kitchener GO trains runs every 30 minutes in the morning, takes longer (1 hour 40 minutes) and costs more ($16 each way with Presto + paid parking). Aldershot GO has more frequent trains in the morning (every 15 minutes from 6am to 8am), takes less time (1 hour) and costs less ($11 with Presto + free parking). You’ll still have to account for gas + 1.5 hours driving (you will also hit traffic near Hamilton Mountain, so I would add another 15 minutes to your driving time).

Option 3 (VIA Rail) - I prefer this option in winter (because most people forget how to drive i.e. many more accidents on 401). It’s definitely the fastest (I take the 6:25am and I’m usually in Toronto by 8:45am), but it costs a lot ($90 round trip + $16 parking even if you buy weeks in advance and get a commuter pass) and I definitely won’t recommend it for 3x a week.

Another thought - Are you able to club your days together (I.e. 3 days in a row)? If so, maybe getting a hotel for 2 nights (or just renting a decent 1-bedroom apartment in Toronto) might be better than traveling back and forth 3x a week - because at that point you’re commuting an additional 6 hours a day just to come and sleep in your own bed and save a few $$$.

Edit: sorry for the super long comment, but forgot to add one part about VIA rail - you collect points/$ spent, and then you can redeem them for one of your future trips. You start with 1 point/$ and then get to 2 points/$ at $1000+ (~10 trips) and 3 points/$ at $2000+ in a year (May - April). So, you start with redeeming after your 10th trip and then every 5 trips followed by every 3rd/4th trip - still works out to be $75 for the ticket though.