Any website do you suggest to use to rent a car in Alsace region?

Have a look at the Auto Europe website.

Yes, Auto Europe, or their sister company Kemwel.

I check auto Europe, but I also check Hertz, Avis and Kayak for prices - then take whatever seems to be the best deal.

One piece of, I think, useful advice: When you search for a car, don't search for a noon pick up or drop off. Most of the French agencies have long lunch hours (typical hours 8 to noon and 2 to 6, but each place varies slightly). Your search won't show anything not open if you search during their lunch hours. Check at either ten in the morning or three in the afternoon and you will get more results. Once you know what's available, you can call and work with the agent directly if it's necessary to pick up or drop off a car during their off hours.

Last time this came up - several months ago, maybe a year - there was only one rental agency in Colmar, probably Europcar. There are more choices in Strasbourg - then only an hour's drive to Colmar, so that may be a better option for you.