I'm a current resident of PR and have taken the ferry 3 times this year to Culebra with no problems. I would go during the week and arrive around 7:30am and wait no more than 2-5 minutes for the tickets.
However, I attempted to take the ferry again to Culebra and it was horrible!!! We went last Thursday and arrived around 7:15am and there was already line. We waited in line for over 2 hours under the hot sun with no shade or tarp to cover us while waiting.
There are only 3 ticket counters, one for Culebra, Vieques, and Cargo. During the wait, I saw one of the ticket representatives fall asleep at the computer, one talk and laugh via cell phone pretty much the whole duration of us waiting, and another constantly leaving their ticket counter. As a resident of this island, I was quite embarrassed of the poor customer service and non existent communication. Nobody knew anything!
I thought it was a holiday weekend but it wasn't. The only difference I can think of from this ferry ride to the past is that the kids are out of school. Perhaps more locals vacation Culebra during the summer break.
Lesson learned...be at the ferry terminal before 7am!!!!