Emiliano Zapata is the only community (of four around the lake) that has any sort of tourism infrastructure, including food, lodging and guide service, and is the place to head whether arriving by bus or boat. On arriving there, you should seek out the presidente de turismo (tourism president), a local officer whose job is to arrange lodging and guides for visitors, and to collect applicable fees, including a US$2.50 daily visitors fee.
The lake itself is a full seven kilometers (4.2 miles) from Emiliano Zapata and accessible only on foot (about 90 minutes, longer in rainy season when the trail is muddy). Along the way, you’re likely to see, or at least hear, saraguatos (howler monkeys) whose other-worldly roar belies their relatively small size.
The trail ends at a long narrow beach, which serves as a jumping-off point for visiting the lake. The best and most popular way to explore Laguna Miramar  is by kayak or cayuco (traditional dugout canoe), both available for rent at the beach (US$10/day). The tourism president also can arrange for a guide (US$8/day) to take you to various sights around the lake, including caves and prehistoric paintings.
It’s worth asking about exploring one of the lake’s islands (some of which have ancient Maya ruins) or hiking in the rainforest on a far side of the lake—unfortunately, those areas are part of neighboring ejidos and may be off-limits to tourists. For the same reason, if you’d like to simply paddle around on your own—a sublime experience, especially once you’re oriented—be sure to confirm where you are and are not permitted to go ashore.
Be aware that from June to October can be quite rainy, which sullies the lake water somewhat, and can turn the dirt trails into a slippery, muddy mess.