Take Garuda, it's on time you can purchase the ticket online and they will allow you 43kgs checkin luggage for your diving stuff..
Wings is only 10kgs luggage allowance (you will have to pay about 2USD per additional k) -also a LionAir subsidiary-, depending on your extra luggage you may pay 20-30USD per pax additional one way, so you end up quite close to Garuda with a lame service and small propeller aircrafts.
My second choice would be Nam but I don't know whether you can purchase the tickets online from their site..THey-re also more friendly with dive equipment, I think you have a 30kg checkin policy incl. dive euipment..
You can easily take the 7:30 AM flight, that's what I did. Bring your computer that will tell your no flight time and just tell the guys on DDK not to push the dives on the last days, they will do accordingly. (remember the Nitrogen accumulation is more about dive length than depth).
Labuan Bajo is not that fun to stay during the day, I know only one good thing to do that is going on a beautiful beach on the bay islands (Bidadari mainly)