Mykul,
They are boarding the pangas from the beach right next to the pier. Yes, you will have to take your shoes off but if you are all going to spend the day on the beach it should not be a problem for you. It just depends on how you want to do it, keep in mind if your entire party is going on the boats you will more than likely not all be able to get on one bus (depending on the time of day you go). So that would mean some are waiting at Boca while the rest of your group is waiting for a bus.
My suggestion would be, if you can arrange it, to take a run down to Boca when you get into town and see if you can arrange for 3 water
taxis that are not running a regular schedule and reserve them for your party. If you just show up it might mean a longer delay trying to get all of you on the boats.
People think it is easy to just show up and get a boat but with a group as big as yours you have an entirely different situation than the tourist that walks up and wants to grab a boat. Trust me when I say with that many people and that many boats involved you are going to have to have some type of reservation/arrangement before you just show up.