How is rotation of gas giants measured ?

With Jupiter. there are many distinct atmospheric features which can be observed over time, and their rotation periods calculated accurately. From this it is easy to calculate the differential rotation and hence relative wind speeds. This is more difficult with the outer gas giants because, as you say, they lack definite cloud features. There are a few atmospheric spots, such as the white spots recently observed on Saturn, and these return accurate periods for that specific latitude. Otherwise, the rotation is measured using the Doppler shift, by putting the spectroscope slit on the preceding and following limbs of the planets and measuring the speed of one limb approaching and the other receding. Even though the disk of Neptune is tiny in a small telescope, it is huge in a large telescope, so it's easy to position the spectroscope slit. I've observed Neptune visually in a 74-inch aperture Cassegrain reflector, and it really is HUGE!