Hi Jeff,
I've been to both twice and would do either again. The first thing to consider is getting there. For Komodo and that area, you can make Bali your international gateway and then it's an easy couple hour flight to Luanbajo or Maumere. If you've never been, spend some time in Bali on either end - it is a magical place (bring an extra suitcase for shopping!).
Sorong is a little more involved from my experience. You can get there from Manado via Singapore - Changi is the the airport to which all others aspire and the connection to Manado is easy from the US with a cushy overnight in Changi. Once in Manado, you can always spend a couple days in Lembeh. The downside here is I've heard the Manado-Sorong flight, while short, is not 100% reliable, especially when it comes to having all your gear travel with you. If you go this way, you might want to build an extra day in to allow for luggage snafu's. Unfortunately, Sorong is, how shall we say, a less picturesque place to hang out than Bali. The other way to Sorong is through Jakarta, overnight there and then Makassar (Ujang Pandang) to Sorong. This is essentially another full travel day. I don't know if you can make it to Sorong going Bali-UPG-Sorong without a forced overnight in UPG.
Diving-wise, they're both great and have their pluses. From my limited experience, you have the chance to see more sharks in Komodo and there's a great manta site at Lang Koi. Horseshoe Bay and Cannibal rock are excellent macro sites and there's also a resident pair of sea eagles who'll provide great photo ops as they fish or pick up scraps from the boat. And of course, there's the dragons.
Rajah Ampat doesn't have a lot of big stuff, except a couple good manta sites. There are however, lots of interesting wide angle opportunities - Boo Island (with it's "windows"), the Passage, a couple jetties, giant fans and big schools of fish if you're lucky. I found my night dives here were far superior to Komodo. The reefs in both places can be lush and fishy.
I've also been on the Cheng Ho. It's huge and comfortable. All the wooden phinisi boats leak to some extent if it starts raining on you, but the Cheng Ho is a sieve. When I was on it, several of us had water in our cabins and they had to have plastic sheets over the charging station. This was two years ago, so I don't know if that's still the case.
PM me if there's anything else I can add.
You will have an awesome trip on either route!
Phil