I would say that based on the two riding schedules, even ignoring the winter aspect, and simply from your perspective of keeping toned, the trainer is going to beat commuting in most circumstances.
Firstly, an hour on the trainer is quite an intense workout. You don't stop pedaling for that entire hour. With commuting there's usually a lot of obstacles and distractions that cause you to stop pedaling such as traffic lights, traffic, and road conditions. On a trainer, it's much more feasible to maintain a hard effort as you don't have things getting in your way. You can also maintain much harder efforts because you don't have to worry about falling off the bike and watching where you are going. Getting that last 30 seconds of a hard effort can sometimes only be achieved by putting your head down, closing your eyes, and pushing through the pain/exhaustion.
I commute as much as possible, as long as there is no snow. However, even adding extra miles into my morning commute, I find it hard to get a really good workout in. Even a 40 minute ride only yields maybe 20 minutes of quality riding at a good heart rate and effort. I definitely enjoy riding on the road more, but if your goal is "decent tone and shape", then you will see much more results sitting on a trainer for 3 hours a week than by commuting, especially if you aren't pushing the limit during the commute.