- Fly: reasonable price, fast, safe, & reliable. Do book at least a couple of weeks before if you come in the high season. You can fly from Denpasar (Bali), but also from Mataram (Lombok) I believe. Check with LionAir.
- Sail: more expensive, slower (at least 2 days & 2 nights), more unreliable & more unsafe compared to flying. But there are some very cool stops on the way, & the sailing trips always includes stops at Komodo & Rinca islands. Same thing, try to book in advance, a week or 2 should be fine. Read more on How to get from Flores to Lombok by sea with stops?
- Bus & ferry: cheap price, slow (36h), unreliable, boring, tiring, & moderately safe (sailing is probably more unsafe). Read more Go from Lombok to Labuan Bajo by bus & ferry, how to?
- Fly & bus & ferry - option 1: fly from Denpasar to Bima with LionAir, and then carry on with bus & ferry. See also Sape to Labuan Bajo, how to?
- Fly & bus & ferry - option 2: fly from Mataram to Sumbawa Besar with LionAir, and then carry on with bus & ferry. See also Sape to Labuan Bajo, how to?
- Fly & bus: fly from Denpasar to Ende with LionAir, and then go by bus to Labuan Bajo (takes about 12h). That's only worth it if you already planned to visit mainland Flores I suppose, you can stop in Bajawa or Ruteng on the way.
- PNI ferry: super cheap (190'000 IDR in 2015), only every 2 weeks, slow (30ich hours), unreliable, totally unsafe, & very uncomfortable (packed). You probably do NOT want to do that! If you do, you can buy ticket at the official ticket office in the harbour.
Once in Labuan Bajo
We predict a three day excursion
What do you plan to do during those days?
Because Komodo national park is also very famous for its exceptional underwater life, so many people do a mix of land excursion (1 day for Komodo & Rinca island) to see the dragons & underwater adventures by diving or snorkeling (1 to 3 days usually) to see Manta Rays, turtles, sharks and more.
Note that it's worth diving in most sites, snorkelling is fine to see the Manta Rays & nice corals but to see more you want to scuba dive. Having at least a PADI open water before going is best, otherwise you will only be allowed on shallow dive sites (10 or 12m deep I believe).
You can be based in Labuan Bajo (a bit of a ugly, smelly, & dusty town) & go every day for an adventure. ie. one day exploring Komodo & Rinca island, then 2 days diving. In 2015, accommodation in LB starts at 100'000 IDR for a double room, day excursion to Komodo & Rinca costs somewhere like 800'000 IDR (, and a day dive (3 dives) costs around 1.2 millions (+ 175'000 IDR park entrance fee for each day). So a total close to 4 millions IDR (100'000 x 3 + 800'000 + 1'200'000 x 2 + 175'000 x 2). That's a lot of money for Indonesian standards but you'll have a blast.
Another solution is to jump on a liveaboard trip (3 days should be enough but do longer if you want to dive more), also going to Komodo & Rinca island but also doing all the dives. This would be more expensive, in 2015 prices start at 600 USD for 3 days (around 8 millions IDR) but it'd definitely be a much more awesome experience. Apart from the fun/pleasure of being on a sailing boat in an incredible place, you'd have the advantage of being able to dive early in the morning (7 or 8am) to enjoy the best conditions & have the opportunity to do night dives. Oh, and you won't miss a thing by not seeing much (or anything) of Labuan Bajo.