What time of year are you thinking of going? Indonesia is not as seasonal as other places, but some areas can be. Your biggest chances of seeing big stuff is probably going to be Komodo National Park and this park is only done from a liveaboard. Some via Bali, some via Flores, a short flight away from Bali. There are lots of flights to Bali from LAX, mostly via Singapore. Singapore Air is great, so is THAI. You can fly to Bali via Bangkok as well. UA has a good flight to Bangkok then you can grab a number of airlines to Bali.
You have lots and lots of land-based diving in North Sulawesi and that is easy to get to via Singapore (flights about three times weekly). Not too much big stuff, but the critters are some of the best anywhere. The resorts are pretty and you have muck diving on one side of the island, and walls with clear blue water on the other. There are not as many liveaboards there as in other places, as the dive sites are relatively close to shore. But Ocean Rover runs there and she's a great boat.
Raja Ampat is on everyone's mind these days too and that is liveaboard for the best diving as well. Bit of a pain to get there, you have to go through Manado for the easiest connection, so from Singapore it takes a 3.5 hour flight, a wait and then another pretty long flight. But, worth the trip. The End of the Earth.
Much of it depends on how much time you have. And what month of course. I hope this helps.