You would want to look at Collision Categories. I am not sure this code below is 100% correct but maybe it will get you started. You can look at the farseer documentation for more on CollisionCategories.
foreach (PhysicsSprite spr in cnvGame.PhysicsObjects.Values)
foreach (Fixture f in spr.BodyObject.FixtureList)
// grapple hook should collide with both bottom and boxes
f.CollisionCategories = Category.Cat2;
f.CollidesWith = Category.Cat1;