We did cruise and stay (but with family that lives there, so no hotel involved, we/they just use the boat like a ferry), anyway, check in to return was definitely possible earlier than 3pm in February--I think we were on around noon (definitely in time for lunch), and told that it was as late as...4? Double check with them when you get off, though, I don't remember 100% but it was later than we thought.
Check in in PPB was fairly slow for us (2.5 hours), especially after 27 hours of travelling from Vancouver, but checking back in on GB is super quick since not too many people are doing it, we didn't wait at all.
Have fun! We just booked again for June, looking forward to it! Freeport is fun, especially if you are going to rent a car and can explore a bit more 🙂