Car Punta de Mita is about an hour drive from Puerto Vallarta. The road is paved all the way and is an easy drive. You can use this google maps location to get to the city center []
The city is quite small and is walkable.
Punta de Mita is the closest point to Marietas Islands, and takes about 20 minutes by boat. When you arrive in town, there is a co-op with a bunch of pangas (boats) waiting for you. For about 2,500 pesos you can take a boat out to the island. When booking a boat, be sure that you ensure you get an English speaking captain, fins, and snorkel gear. Sometimes the person you make a deal with will not be the captain of your boat.
You first get into the boat, and head out about 20 minutes to Marietas Islands. From there, your boat checks in with the Mexican government and you show your wristband pass (the Panga will ensure you have one). Once the check-in happens, you are brought to an area where you get out of the boat and swim 100 members under a cave onto the beach. With this, be sure that you come to Marietas Islands when the tide is going from high tide to low tide []. If the high tide of the day is 9:20am, and the low tide is 3:30pm, it would be safe to venture out at 11am as it would be mid tide going down. The reason is when you swim under the cave, it may be inaccessible during high tide.
After the 100 meter swim, you will be on a beach. On the right side is an enclosed cave area, but on the left side you can venture out and go underneath a cave to see more rock formations. However be careful as the tide coming in can be powerful and the rocks on the bottom are jagged. Also if you want to take photos, be sure to buy the plastic case from the vendors at the port, or bring a water resistant case. With your panga, there should be a guide with you. People usually stay about 15 minutes at the beach.
Next, the panga should take you to a snorkeling spot on the other side of the island. Lastly, you get a tour of the island looking at some formations, then you head back. When at the island, be sure to look for the blue footed bird.
Note that Marietas Island is due to temporarily close on May 9th, 2016 []