Pelni offer a ferry service from Bali (Padang Bai) to Sulewesi that stops off in Lombok (Lembar as well as Mataram I think) and Flores (Labuan Bajo).
It takes quite a few days to do though, I think it may also stop in Sumba.
We looked at this route last year but then decided the short flights on Lion Air meant more time on the ground for play. We saw the Pelni car ferry in Labuan Bajo and it looked quite decent. over 6 years ago