I went overland from Senggigi (Lombok) with a ticket I bought from Perama. The trip to Flores was utterly grueling, taking about 36 hours to arrive in Labuanbajo. I returned to DPS with a Merpati flight from Maumere. The pilot was kind enough to fly a couple of circles around Kelimutu, which is stunning from the air.
You can find all kinds of boat operators in Labuanbajo who will take you to Rinca and Komodo to see the dragons.
Flores is a real gem of an island - I highly recommend spending some time there.