The times have changed, very few passenger ferries crossing the seas anymore.
And much harder these days to get to go along on any cargo boats, too. Problem with illegal immigration, and the ´war against terror´ arent making that any easier in the future.
We travelled with a Czech couple in Iran & Pakistan, and they said they knew about a ferry (or some kind of vessel, where you can put your vehicle - they had a 4x4, and you can travel on the same boat) between Chennai and Singapore.
They even had an Indian cellphone number to someone, who was supposed to know more, and I tried to call there a couple of times, but no answer.
No-one in Chennai knew anything about such a service. Frankly, I dont think it exists. Someone said there once was a regular ferry to Penang (Malaysia) but that was in the 1980´s.
Sure it might be worth to ask around, if you got time then who knows, maybe you can find some suitable ship going the right way at the right time, accepting to take you and the bike, but its still a slim chance. Freighting the bike & flying yourself is the normal way to go these days (a big hassle, I know!)
I think there is a ferry from Chennai (and maybe from near Kolkata, too?) to the Andaman&Nicobar islands. That is a lot closer to Thailand and Malaysia than mainland India is. But how do you get onwards from there, I really have no idea. And if you end up freighting the bike from there, that is probably going to cost more than if you did that in Chennai or Kolkata, for example.