The floating markets are a very lively scene, accommodating much of the goods exchange throughout the area, and can be quite freely visited on board smaller boats for about US$5/hour per boat. You may take a tour from the Ninh Kiều pier, where the "boat ladies" are charmingly eager to welcome you aboard. On January 2013, starting prices are about 15$/25$ for 3h/7h tour with either one market + canal, either multiples markets + canal.It could be bargained down. Pay attention as there is an old pushy lady haunting tourists at the riverside to sell boat tours. Best to get your tour directly from a boat driver.
Cai Rang (Cái Răng) floating market is the main wholesale floating market near Can Tho. Go there early in the morning (as early as 5:30am), and come back through the small tributaries to Can Tho river; about 3-4 hours. The Mystic sampans offer higher-end breakfast cruises to Cai Rang floating market.
Phong Dien (Phong Điền) is further upstream the Can Tho river, and worth seeing as it is a retail market. It is very active at dawn, but slows down early too, so you may want to go there by land. The arroyos back to Can Tho are also very much worth a ride on a small boat.
Phung Hiep (Phụng Hiệp) is much farther away, in the neighboring Hậu Giang province, but deserves a trip if you are going to stay more than a few days, as it is always bustling with activity.
Tra On (Trà Ôn), in Vinh Long province, is just over an hour downstream the Bassac (the lower Mekong branch, also called Hậu Giang or Sông Hậu). It is a small floating village's market anchored near the clouds' island (Cù Lao Mây).