Lake Como or Lake Garda

We are finding many places in Europe are being overrun with the tourists

Be part of the solution and stay home?

Not been to Lake Garda, but have been to Lake Como, stayed in Varenna, and found it a wonderful experience.
Cannot image Lake Como being a 'bad' or lesser choice as a lake destination.

Earl,

My suggestion would be either Lago di Como or Lago Maggiore. Lago di Garda has it's charms but only the south end is served by rail service (Peschiera del Garda and Desenzano), and you'd need to travel by car, bus or ferry to reach towns on the north end, such as Malcesine or Limone sul Garda.

There are some good day trip possibilities along Lago Maggiore. If staying in Stresa, you could (for example) travel to Domodossola and then take the scenic Cento Valli Railway to Locarno (CH) and then return in the evening by boat. You could also take the cable car up to Mount Mottarone or visit the beautiful Borromeo Islands (very short boat trip).

I don't think you could go wrong with a visit to either Lake Garda or Lake Como. Or Lake Maggiore for that matter. I have visited all three several times each and enjoyed my time at each lake. There are multiple small towns to be visited from each lake. I would do some research on all three and see if one of them captures your interest more than the others. My personal favorite is Lake Garda but it is really a close call between them. I have never visited in the fall so don't have any sense of how crowded they may be. I have been to each in Spring and Summer and never felt like I was crowded - except maybe during the day in Sirmione (Lake Garda) though evenings there were quite lovely. Happy planning!

Why not both?
You could do 3 nights on lake Como. I recommend one of the 3 main towns in the midlake (Varenna, Bellagio, or Menaggio), which are connected by frequent ferries in minutes.
Then you could stay 3 nights at lake Garda. However for lake Garda you might need 4 nights, depending on what you want to visit. The lake is larger and some interesting locations are at the opposite ends (like Sirmione and Limone) so it takes longer to travel from one side to the other.
I recommend Malcesine as a base for lake Garda. Mt. Baldo, up above Malcesine, offers great views too

I agree with Ken re Stresa and Lago Maggiore. You can take a boat to 3 outlying islands, each unique. Or travel further afield by boat to Villa Taranto and tour the gardens. In Stresa I stay out of the center a little bit as the walk along the brick promenade lakeside is so beautiful- then I’m hungry by the time I get into town! A very modest Hotel Fontina is a family run place I’ve stayed in many times. Good luck.

I've been to all three and they are all interesting with lots of small towns and great scenery. Lake Como is the most popular with Americans and especially the mid lake region (Bellagio, Varrenna) and is usually the most crowded. Lake Garda (especially the northern section) is very popular with Germans but still probably less crowded than Lake Como. But by late Sept early Oct it shouldn't be too bad.

Here's my photos of the different lakes - https://andiamo.zenfolio.com/f405234590