In general, does you wife just want to pick up some makeup at good price or she wants service like free facial?
For the price: Local drugstore will be the best for Shiseido, Kose, Kanebo or other Japanese brands makeup + skincare. Because it carries more lower end product lines + more variety and more cute/seasonal/limited products. Also, drugstore offers discounts on the MSRP of these brands while department store doesn't.
Department store offers service and point system. Everything is marked at MSRP but if you buy certain amount (let's say 40,000 yen) they will offer you free facial and the SA is way more generous on giving away samples. Also department store tends to carry premium lines or mid-price line of each brand only.
Duty free shop is nice but product lines available is limited and often very crowded. Unless you clearly know what you want and the usual price level, don't suggest you to buy there. I bought Shiseido fake eyelash for 1260 yen in local drug store and saw the same thing at duty free for 1200 yen. I was happy to buy at drug store as I browsed around there for 2+ hrs trying everything on w/o any hassle, not sure I had that much time in the airport.
PS I bought makeup+skincare in Nagasaki drugstore, Iwataya Fukuoka (department store) and Narita Airport Duty Free about 2 weeks ago.