We haven't booked yet (mainly because I want to have the transit situation squared up at least in theory before we commit to going there), but we're planning to book at Sand Sea. Rayavadee looks incredible, but it's a bit too pricy for us!
We're not terribly worried about jumping in and out of the water with luggage (our suitcases have straps and a hip belt for wearing them as packs), it's more the other issue you mentioned -- safety and availability of boats.
I saw that info on the Princess ferry, which is what led me to their site directly. The writeup seems to be a few years old and I was nervous about things having changed. It seems like the safest thing would be to fly into Krabi the same night we land in Bangkok (not ideal, but oh well), and then to get the ferry in the morning. In any case, the specifics on booking on the actual ferry website are either not translated well or vague enough that I'm still a bit unsure! If only I could read Thai...