According to the wikipedia article above, Madagascar was settled very late (almost in the ADs), and was first settled by Austronesians arriving in canoes from Borneo. Borneo is very far from Madagascar - how is this possible?
I'm not sure how to answer this except to say that the outrigger canoes used by Austronesians to settle both Madagascar and all of Oceania were pieces of technology extremely well-suited to their purpose. There wasn't a single design that was utilized across space and time -- canoes were made in various sizes and with various minor differences -- but they were well-constructed, stable vessels that were effective for either short, medium, or long distance travel. Obviously longer voyages, like the voyage from Southeast Asia to Madagascar, carried a certain level of risk. But the results speak for themselves, I suppose.
This is a well-covered topic, and a point of entry for a lot of people into Pacific Islands history and culture. If you're interested in reading further, there are plenty of sources to check out. Here's one that I like:
D’Arcy, Paul. The People of the Sea: Environment, Identity, and History in Oceania. Honolulu, Hawaii: University of Hawaii Press, 2006.
In terms of the settlement of Madagascar specifically, I can't help much more I am afraid, but I can quote what I said last time this question came up:
I believe there is some evidence (mainly based on boat-building techniques which are similar to Austronesian ones in some ways and unlike those found in South Asia) that they briefly settled in the Maldives, or at least passed through. I think the main person to write on this is Pierre-Yves Manguin.
I do believe that it's generally accepted that Madagascar was settled through hopping along the coast of the Indian Ocean. I believe Alexander Adelaar has done quite a bit of work on the Austronesian migration to Madagascar.
I'm not sure about Western Austronesia, but you certainly shouldn't confuse Polynesian and Micronesian canoes with the small boats used on rivers. The biggest ones for ocean travel were small ships. The biggest Tongan war canoes could hold around 100 people as well as supplies for a long voyage and took over a year to build. See We, The Navigators by David Lewis and take a look at this picture of a Maori canoe, which were not even as big.
