Is there a gluten free alternative for flour in clam or mussel chowder? The recipe calls for a couple spoonfuls.
Yes, certainly. The flour is only there for thickening. You can use pretty much any flour or starch from a gluten-free grain or tuber, and it will thicken just as well.
Depending on whether you want to add another flavor, you can go for a flour with a strong taste on its own, like buckwheat, and/or whole grain flour. If you don't want that, go for a starch.
As for the amount, do a 1:1 substitute by weight. You can employ it with whatever technique is prescribed in the original - a roux, a slurry, or dusting the solid pieces before adding them, it will all work.