From Masaya, there are two daily buses that will take you to the waterfront of Laguna de Apoyo. These usually leave around 10:30 a.m. and 3:30 p.m. and arrive an hour later. They then turn around for the return trip. If you miss these, the “El Valle” bus will take you to the crater's rim, where it's a 45 minute walk to the waterfront.
From Granada, Mayasa-bound buses should be able to drop you at “la entrada de la laguna” (the entrance to the lagoon). From here it's about a 90 minute walk to the waterfront, or you can catch a taxi.
Taxis direct from Granada should cost $12 - $15, taxis from Masaya will be $8 - $10.
There are private shuttles organized by Bearded Monkey Hostel, and Hostal Oasis. These leave most mornings, and should be booked the night before. The shuttles cost $2 per person each way.