Thônes is an attractive small town, with a lovely mountain backdrop and a very convenient location to tour the area between Annecy and Chamonix. Accommodation tends to be much more affordable than on lake Annecy or in the mountain resorts, and there are plenty of shops and restaurants in the town so, if your accommodation is central enough, there is no need to drive everywhere.
Now, is Thônes the most postcard-perfect town/village in the region? It is not. It is a place where people live and work, with several factories (furniture mostly, no smell/fumes), supermarkets, etc. Have a look at Google Street View, coverage is very thorough.
For a more "quintessentially alpine" experience, the villages of Manigod and Le Grand Bornand, higher up in the mountains above Thônes, have plenty of chalet-style rental properties. They are very expensive in summer, and they tend to be large. Also, the villages are spread out and most places require a car even to buy some bread (that's the most French criteria ever). But if you have second thoughts about Thônes, check Le Grand Bornand and see what you find. La Clusaz is another option, but I do not like the village as much (some not-so-pretty resort buildings there, and very intrusive skiing lifts in the landscape).
You could also go down towards the lake (Talloires, Menthon), but demand far exceeds supply, anything with a lake view will cost dearly, and crowds+traffic can be annoying.
In short: if you found accommodation you like, at a price you like, in Thônes, you will have a good time and you should stick with it. But comparing with that you can find in other nearby villages is free!
