There are boats going everyday:
Except for the Singapore-Batam, information can be hard to find, but I took all of those boats in a not too distant past.
I know there are visa on arrival at Dumai and Batam. Probably also at Tanjung Balai (They have at least basic immigration. I was traveling from Indonesia).
Technically, I should also mention a ferry from Tawau to Tarakan (no visa on arrival when I was there, but it was in 2012) in case you go to Borneo.
According to Lonely Planet, Malaysia to Indonesia by ferry can be a bit dicey. Some cursory other research does not look promising either.
I would recommend taking AirAsia from Kuala Lumpur to Medan or Pekanbaru. It might be slightly pricier than a ferry but would be more convenient and have a lower likelihood of immigration related friction.
There is a ferry from Singapore to Batam island, but I don’t think that’s what you have in mind.
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