Flores island is small enough to walk across in fifteen minutes. Santa Elena, just across the causeway, is best reached by tuk-tuk (a few quetzales) or on foot.
Shuttles to Tikal leave at 5am, 8am, and 2pm from various hotels and travel agencies on the island — book the day before. The 5am run is the one to take if you want to be at the ruins as the mist lifts; buses come back through the afternoon until the last departure at around 5pm. For the lake itself, lancha (small motorboat) tours leave from the eastern docks; they will quote per person or per boat. Negotiate firmly.