We stayed at the GF last week, our first time at a monorail hotel, and found the ferry system to be inefficient and frustrating, so we didn't take it at all unless forced to - which we were in the last day due to a MR outage.
First night, we tried to take it from MK to GF. After waiting awhile, my three year old decided she needed the bathroom. The boat was still there when we got back and it wasn't full, yet they were just "casting off" and couldn't get us onboard. We took the MR back.
The next day we decided to try it from GF to MK. We waited awhile before it came, then learned it stopped at the Poly afterwards. I'm sure this is well-known but it wasn't to us. We were still waiting for the ferry at GF when we saw a MR go by, so we could have gotten there in the time it took to even board the boat. The trip cut too close to our first FP window, so I rebooked it once I realized we were on our way to the Poly (would have made it easy with the MR). We also had to fold down our stroller, which was not required on the MR.
After that, we avoided the ferries until the last day. We checked out and took the MR to MK for a few hours before our DME scheduled pickup at 3:50. Around 2:30, we headed back only to find all MR trains were out of service. There was already a long line waiting for the GF/Poly boat, but we didn't have much choice but to get in line and wait (we were told there were buses available but we felt it was safer to wait for the option we knew, rather than try to find a bus, stop at multiple hotels, etc.). We waited about 20 minutes until a tiny 30-40 person ferry showed up (the kind with the canopy and wood seats). They filled half the boat with scooters and wheelchairs first, then a few from the line, which was probably a couple hundred deep by then. Up to that point, we were waiting in shade, but this now forced us into the sun where we waited for another 20 minutes. In the meantime, we were seeing big boats at other docks leaving maybe 20% full with barely any lines. The next boat was bigger (could handle 140) and after some stressing, we made it on. The line was now probably about 400 deep, backed all the way to where the MR ramp starts. We finally got back to the GF with about 10 minutes to spare for our bus ride.
My biggest complaints were that there was no warning of the upcoming outage earlier; if it was unplanned outage, they should have out more boats in circulation; they should adjust the size of the boats going to the GF/Poly; and they should cover the entire waiting area. I can't imagine what it would be like if this happened in July. The CM on the dock also didn't walk along the line to reassure people - there was zero communication, no posted boat schedule, etc.
So...long story short, if you have a hard deadline to get back to the resort or another destination, allow PLENTY of time just in case the MR is out!