if a monster is granting combat advantage, can a rogue make a sneak attack with a thrown dagger?
Yes, as long as you have combat advantage and you attack with the appropriate weapon you can deal sneak attack damage. You are no longer required to flank. Flanking is just the easiest way to get combat advantage.
Note, however, that a flanked creature only grants combat advantage to the creatures flanking it. So if your two buddies have flanked a monster, you can't stand back and sneak attack it with ranged attacks.