It's not possible for trains around the CT region to be "booked up" as the majority are regionale trains. Schedules for those on Trenitalia are not available more than a week in advance but change very little so pick a day of the week - within the next seven days - and plug in a journey between any two of the villages to see a fairly accurate sample. As this is the off season, there may be more runs during high season. Tickets are only a couple of euros or so for each journey - depending on distance - so buy them when you get there. It's also possible to purchase a combo one or two-day trail/train pass for use of the trails and public transport but I don't recommend one of these if you're not planning to hike.
http://www.parconazionale5terre.it/Ecinque-terre-card.php
Trains are the most efficient way to get around and, as Laurel said, take only a few minutes from village to village: the entire distance from southernmost Riomaggiore to northernmost Monterosso is only 7 miles. And as she also said, driving/parking is a real pain so a lot of people leave their cars in La Spezia and take the train in from there (also a short/ inexpensive journey). Tickets MUST BE VALIDATED before getting on the trains, and the authorities are especially eagle-eyed here so be sure and do that as fines are expensive for having an invalid ticket.
You can take trains to all of the villages but Corniglia's station is at the bottom of the cliffs the village is perched upon. If you don't wish to make a strenuous climb, there's a green bus that runs between train station and village, and costs just a couple of euros if you don't have a pass. For fun, take the long stairway back down to the station as it's a lot easier than going UP!
Ferries run to all of the villages but Corniglia but are not the most efficient way to get around.
Expect both the trains and ferries to be VERY busy in June.
There are many trails in the park but the one you're probably thinking of - as it's the most popular - is the Sentiero Azzurro. It has 4 segments, and not all of them have been open over the past few years. I expect the section between Corniglia and Manarola to remain closed this year, the Via dell'Amore (between Manarola and Riomaggiore) may or may not be open; too early to tell.
You can check trail status at any time on the park's website:
http://www.parconazionale5terre.it/Esentieri-outdoor.php
The Sentiero Azzurro segments are 592-1 (SVA2) to 592-4 (SVA2) on the chart, and red-and-white circles mean that a segment is closed. This route is not "backpacker" difficulty but also not an easy stroll: expect lots of long, steep steps and grades to maneuver, and its going to be very busy.