I was able to talk with someone at the Port Authority about the ferries to Culebra and Vieques today, so I will share the info.
The ferries run every day- even holidays. You can make your reservation as far in advance as you want- there is no time limit.
You reserve by credit card. On the day you are taking the ferry, you go to a special window on the side of all the lines to get your reserved tickets.
To make reservations call 1 -800- 981-2005 M-F from 8-11a or 1-3p.
Be VERY patient- I probably tried calling 20 times before I got a person.
You can call that number to get current ferry schedules via an automated service (no human needed!).