Is he painting them or powder coating them? If he is powder coating them I would have him do it, not sure if that price includes him taking apart and putting back together the caliper for the coating process. If it were $100 to paint them, I would pull them off and tape them off nicely and paint them myself with some red caliper paint for under $10 and have the satisfaction of doing the job myself, then treat myself and the wife to a nice dinner or some more go-fast parts with the remaining $90
Either way you choose, I'm sure they will look nice. And like most people stated, I personally wouldn't do covers, to me they just look cheap and out of place. That's just my 2 cents.