Central Panajachel is walkable. Calle Santander, the lakefront, and the main docks are close together, though traffic and uneven pavements make walking less relaxing than it should be. Tuk-tuks are cheap for short hops, including the ride to Reserva Natural Atitlán.
For other lake towns, use shared lanchas. Confirm the destination before boarding, keep small bills ready, and expect prices to be higher for foreigners than for local commuters.