We were just at the Polynesian in July and were able to check our luggage in at the airline check-in that's in the lobby. They transfer your luggage directly to your flight. They were able to check my other carryon bags at the hotel until we were ready to be picked up by Magical Express (which usually picks you up about 3 hours before your flight leaves). We were able to check out, spend the entire day at MK (luggage free) and be back at the hotel by 4:00 for the bus.
If you're not doing Magical Express and/or they don't have airline check-in at your hotel, you can check your lugguge with the hotel and they can hold it until it's time for you to leave for the airport. All Disney hotels do this service. It's perfectly safe - we checked in our laptop, camcorder etc (in a bag, of course) and everything was intact when we returned.
I would give yourself a good hour (if not a little more) to get back to the hotel from where you are and get your luggage before you need to leave.(if you're driving directly to the airport it's about 30-40 minutes to get there)
Have fun.