There are plenty of resorts, as mentioned (RA biodiversity, Papuap Explorers, Kir Eco, Sordido Bay, Misool Eco resort, and so on). I would personally be very hesitant to stay with a Homestay if diving is your top priority - this is a very remote area, and I simply don't trust very small operations / homestays to have properly maintained fill stations and safety measures (O2 on board, fast boat / radio to get you to the Deco chamber if necessary, experienced guides, etc.). The resorts do. We had a great time at Papupa Explorers, which is a very nice resort and at the lower end of the price scale for that area.
For Komodo, we took a day boat out twice, but I would either stay at a resort deeper in the park, or do a liveaboard next time. And do some reading on which ones. We had a few great and a few 'meh' dives at Komodo, in part because Labuan Bajo is pretty far from the dive sites (so long boat ride out) and because the day boats serve a lot of backpackers, so they tailor the trip to the level of diver present. We were with several folks who had only just completed their open water dives, and some of the current / drift dives were clearly beyond their ability and comfort zone, so we ended up doing some very, very average dives because of that. The liveaboards will tend to attract slightly more hardcore divers.
The two land-based operations in Komodo that looked interesting to us were Scuba Junkies (were full when we were there) and, at the other end of the price spectrum, Komodo Resort (in the park), which we heard very positive stories about from a fellow diver at Papua Explorers.
In terms of itinerary, if you only have 2 weeks, pick one of the two destinations. We had 3, and spent 1 week in RA, 1 week doing land-based stuff on Flores and 2 days of diving in Komodo, starting the trip with a bit of acclimatisation on Bali for a few days. It was a fantastic vacation, but it was really too busy by half. Next time (and there will be a next time!) I would say 10 to 14 days in Raja Ampat (maybe liveaboard, but the resort life is pretty relaxing, with your own personal pondok and hammock), and then maybe a week of doing very little except galivanting around on another island (Bali, Lombok, lots of choices).
