Has there ever been a seaplane with retractable pontoons?
There have been a couple of examples- the Blackburn B-20, for example, had a retractable pontoon below the hull (and retractable wing floats), though it was an one-off experimental aircraft with a single flight to its credit. 



Blackburn B20, image from dinger.byethost5.com

As a more widespread example, the Consolidated PBY Catalina's wing floats were retracted electrically after takeoff.



Catalina's retractable wing float; image from navy.memorieshop.com

Retractable floats have been used in other aircraft too- like the Grumman G21A Goose and the SL-12C amphibian. Some designs like the Kawanishi E15K featured retractable floats, which were later removed due to issues.

A little more digging reveals that the German Ursinus Gotha WD 10 Fighter Seaplane had retractable floats quite early- during WWI!. However, I doubt it counts as the aircraft never went past taxiing stage.



Ursinus WD 10 fighter seaplane, image from 1000aircraftphotos.com