For us, I would:
Take the WL boat to MK (you will go through security at the MK dock) then MK/GF/Poly boat to GF.
On the way back, take the Resort Monorail from GF to MK (it’s just one stop), then boat from MK to WL. You’ll go though security at the GF monorail station.
There are other options, but this is generally the most direct in terms of Disney transport options. And a quite pleasant journey (unless the weather is bad).
I’d have a plan B (such as Minnie Van) if running late or weather is a problem.