mooball is right about Perama Tours - they're the cheapest boats there, but not necessarily the safest. (a travel blogger's boat sank last year - http://www.adventurouskate.com/adventurous-kate-gets-shipwrecked-in-indonesia/)
But obviously there are no buses! Bali and Flores are two very separate islands...
When I visited Flores, I flew from Bali to Labuan Bajo. Then I chartered a boat for 2 nights / 3 days of cruising to Komodo and Rinca Islands. For 2 people it wasn't that much more expensive than joining a tour.
I believe there are bus trips you can take from Lombok to Flores (via Sumbawa). It's a very long overnight journey. I think it was Tezza who did a trip report on it a couple of years ago. Search the forum...
I was quoted 440,000 for the trip from Denpasar to Labuan Bajo and no one knew for sure how long it would take to get there but somewhere around 24hours. The problem is when travelling that far by bus across all those islands is that drivers change, buses change, destinations change without any one single person knowing what's going on. I would think you'd be fairly lucky if the bus you departed Bali on was the bus you arrived in Flores on, but the people at the bus station say it's possible.
So you'll more than likely get on a bus that allegedly goes all the way to Flores according to the driver, but may not. The only way to handle it is to just wing it. Get on the bus and see what happens. It'll be an experience.
About 6 months ago I took the Kencana boat from Labuanbajo on Flores via Rinca and Komodo to Lombok (from where you can easily get the ferry to Bali - actually the "cruise" finishes on the east side but included is a road transfer to Mataram on the west, not too far from the ferry port). www.kencanaadventure.com
I was a bit hesitant initially as it was hard to find much positive information online and also being aware of Perama's accident a few months prior. Perama and Kencana seemed to be much of a muchness in terms of quality and I wouldn't say either would be deemed "safer" than the other; the accident did happen at a time of year when waters are notoriously choppy but it could happen with any company at any time - you should make it your responsibility to check for yourself that the boat carries sufficient life jackets for all passengers and crew and looks as sea-worthy as you can ascertain BEFORE you set sail. The main reason I chose Kencana was that their boats stop at both Rinca and Komodo whereas Perama stops at only one depending on whether it's the east to west or west to east sailing.
For the 3 night trip we paid 1.5 million rupiah (about £150/$175) per person which included all meals, tea/coffee, 1 large bottle of water per day and National Park entrance and snorkelling fees. The only extra we had to pay was the Rp50,000 camera fee (payable once and valid for both Rinca and Komdo). Snorkels and masks were provided. Meals were good - far better than I expected and there was plenty of food. In addition to the dragons, the scenery on the cruise is absolutely stunning and the snorkelling was fantastic. Sleeping arrangments are simple - mattresses on the upper deck.
We were really lucky as there were only 4 of us booked on our departure so we had plenty of room (I'm sure this contributed greatly to the overall experience) whereas on a busy boat I suspect you would be fighting for space to stretch out - as well as space to sleep! I would definitely recommend going from Flores to Lombok as the boats in the opposite direction all seemed to be a lot busier; the cruises get a big push from travel agents on the Gilli Islands. The cruise is far from luxurious but I think it's good value for what you get and if you don't have massively high expectations of the quality and focus on the amazing surroundings you will have a positive experience. To make it as safe as possible I also woudn't do it in the rainy season.
I also had the same question time ago and decide for take a boat to Flores. I traveled with Blue Water Cruises.
They offer different packeges from 4 until 7 days going from Lombok to Flores...depends of if you want to see other islands or just direct to Flores.
I took one for 5 days and could visit Moyo, Santona and Komodo (Flores) in one trip...with enough time to get a look in the island and snorkeling. And then I staid in Flores for a while and flew back to Bali by plane.
Nice experience Can only recommend it
#9 Katkat has been a member since 3/4/2012. Posts: 4
We did the overland option (with a few ferries obviously) and it wasn't so bad, although in the end I don't think it saves enough money to justify the time spent: http://erohisms.com/overland-travel-from-bali-to-flores/
Here's our Flores trip report as well: http://erohisms.com/the-ups-and-downs-of-one-week-in-flores-aka-does-the-emperor-have-clothes/
#10 erohisms has been a member since 17/3/2013. Posts: 10
I'm not sure the standard backpacker boats that do this run could do it. Some are quite large though. I saw these two at Pulau Satonda on my recent trip in Sumbawa and you can see they're certainly big enough to put a scooter in -- but I don't know if they'd do it... Maybe contact an operator and see what they say.