I've had bad luck with free-floating pellets clearing, so I either use whole hops or put my pellets into a bag for dry hopping (you can get a ton of women's nylon stockings at a dollar store or whatever for next to nothing--use them as disposable hop bags).
Without a hop bag. I've wound up siphoning out from under the top floating layer of dry hops, and losing a little bit of beer by stopping siphoning when the layer containing hop flakes reaches the bottom. A few little hop flakes in the bottle aren't a big deal, other than maybe aesthetically.
If you're averse to that, finings (e.g. gelatin, available at the supermarket) and cold crashing may help.
Some people have successfully put a strainer bag around the bottom of the autosiphon when transferring, too. Keep it lose and away from the intake to stop it from clogging.