Right now, the airport in Marinduque is still being expanded and improved. Hopefully, it will be done soon so flights can resume. Trust me, you will always prefer the 30-minute flight over the road/RoRo trip.... unless maybe you're with a group of friends who like roughing it and intend on bringing A LOT of stuff.
Those who don't have cars can also opt to just board buses at Buendia... but I am not so familiar with the fares for that option.
What we did last Holy Week was go via what they call door-to-door, wherein a van fetches you from your home and delivers you to your accommodations in Marinduque (those going to Bellaroca are probably fetched at a certain jump off point).
A usual door-to-door van's maximum capacity is 16. They insist on 4 persons occupying the three rows of seats while 2 people sit with the driver in front. The one we used charged P800/passenger. You can also rent their van for P11,000 for an exclusive trip (say, you don't want other passengers coming with your group... or your cargo will occupy the space of the entire van).
For those with private cars, the charge per car at the RoRo ferry is P2,900 (with 2 passengers free, the rest will pay P220 if Balanacan port bound and P340 if Cawit bound). Cawit port is currently closed though so all ferries dock at Balanacan.
Now, for those who want to hire a van for a day tour in Marinduque... it will cost P2,500. Boat hire to Tres Reyes Islands is P1,500 (or P300/day depending on the season).
Going to Marinduque and coming from Manila meant that we were among those who were picked up first (around 4 PM). Unfortunately, at 10 PM, we were still fetching passengers from Laguna! This isn't always the case, it will depend on where the passengers are coming from and if the driver will be fetching many passengers from one place or just one to two passengers from each point. Sometimes, you'll be lucky... sometimes, you'll want to just go back home.
Usually, the door-to-door travels at night and catches the 12 midnight ferry in Quezon, and you will be in your destination in Marinduque between 3-5 AM.
Going back to Manila immediately after Holy Week proved a bad idea for us... because there were so many vehicles waiting to be ferried that we were stranded in the passenger terminal building for over 12 hours. We were fetched at past 2 PM and were in queue at 5... but got to board a ferry at almost 9 AM the following day. Talk about hassle! :) And since we're from Manila, we had to be patient as the driver dropped off half of the passenger load which can prove exhausting to ones already so tired (and with kids too).
There's now a park and sail option at the Quezon port. You can leave your car, board the ferry and just ride a jeep at the port to your destination.
Others coming from Marinduque also have the option to just ride the jeep to Balanacan and then board a door to door van there which will bring them to their doorsteps in Manila. Just not sure how much the fare is for that setup.
Come to Marinduque so you'll know how wonderful the springs and lakes and mountains and beach strips that await you :)