If you were not at a monorail resort, I might feel differently, but since you are, you should be fine.
If your flight arrives close to 3:30, you should be at the Polynesian no later than 5...and that's the outside time. I would imagine you would be there by 4:30-4:45ish. But, even if you arrive at 5, you can get checked in, freshen up and then over to MK and Crystal Palace by 6. Shouldn't be a big issue. Just don't linger and take your time.