I've been to both, and am returning to the CY on Friday for 10 days.
It really depends on what you are going to do.
If you are a pool and/or spa person then I would recommend the Marriott as it has 2 pools and a snack bar, and a very nice Spa. Marriott is at the east end of the main drag in Waikiki.
Courtyard has free WiFi, smaller pool than the Marriott. Courtyard is just over a block off the west end of the main drag in Waikiki.
It takes about the same time to walk from either to Dukes.
I was there back in July and spent 4 nights at each. I used the pool at the Marriott for about a half hour one day. My main reason for going to Hawaii is to visit friends who live there and Waikiki is convenient middle ground as one friend lives in Eva Beach, another on Kailua Bay, and a third on the hills overlooking Diamond Head and Koko Head.