Yes the luggage is stored safely in dry places (placed by staff at the water taxi). The boat may be crowded and the seating is not necessarily the most comfortable. This would be another adventure in your travels. As stated by others, you do have to get from the International airport to the water taxi but for a large group the savings make it worth it. It will depend on what time your flight arrives as to whether or not you have enough time to catch the boat. As another poster mentioned, flying from Municipal is also cheaper (almost half price) but it also involves a taxi. Not sure if you can make reservations on the water taxi from the states but it would be worth checking since they can be very busy. Good luck on your decision and keep us posted on what you decide.
Enjoy San Pedro
WOW Elbert the taxi fares must have doubled in two years. It cost me $25US.
Another option is Tropic Ferry. I have not used this service but friends swear by it. http://tropicferry.com/