That's a tough choice, I liked both. We did stay one night in Colmar, but stayed in Eguisheim for the additional nights in Alsace. Colmar is charming, but it is a bigish city. There are smaller, cuter towns in Alsace. We followed the wine route and had a really great time driving through the charming towns with grapes growing along side the roads. I also really liked Salzburg. Its is a beautiful city with a lot of charm, history and for Sound of Music buffs it is a must do. If you really like wines, especially drier reisling type wines, I'd go to Alsace, if you are less interested in wine, I'd choose Salzburg. If you had more time, I'd say do both.
And I'm just noting that you will have been in Moselle. The wine in Alsace will be similar in variety to Moselle. The Alsatian scenery will be similar to the Moselle without the river.