Chintheche is small enough that you can walk between the beach lodges and the town centre without difficulty. Most visitors spend the majority of their time on or near the water, so there is little need for organised transport.
For trips along the lakeshore to neighbouring villages or to the main road junction, motorcycle taxis (locally called "moto") are the standard option. They wait near the town market and are cheap by any measure. Agree on the fare before you set off.
If you want to explore further afield — to Nkhata Bay, the Viphya Plateau, or more remote stretches of beach — it is worth hiring a car in Mzuzu or organising a day trip through your lodge. Most guesthouses can arrange this informally, and the Chintheche Inn is particularly well set up for helping guests with onward logistics.