I think either could work. We've actually done both recently. A few years ago, the cheapest flight had us landing at about 9am. After checking in, we went to MK. Our daughter was almost 4 at the time. We stayed til about 5, basically just using our 3 FPs, meeting a few characters, taking lots of pictures. It was a nice start to the vacation. We made sure she went to bed on time and was refreshed for the next day. She did miss her nap that day but was so excited, she was fine throughout the day.
On our last trip this past Sept, we landed a little later, closer to noon, so we decided to just stay at the hotel. We walked around the resort, swam in the pool, checked out the gift shop, ate in the food court. It was also a nice start. And again, we made sure our girls (now 5 1/2 and 1) went to bed at their normal time to prepare for a busy day the following day.
I think either option would work! Because this is a shorter trip for you, if it were me, I'd go with the earlier flight and either do a few hours at a park or a character meal at a resort. Or even Disney Springs.