Whether or not all the Stormtroopers were clones by 0ABY, the Empire did and does use non-clones to bulk out the Stormtrooper ranks.
Additionally, many Stormtroopers are not Kamino clones, but the quicker-grown Spaarti clones. The Spaarti process is not as effective and the quality is not as good. There is much more variance in Spaarti clones than Kamino clones. The troopers thus created are still exceptional soldiers, but they are not the well-trained and flexible Clone Troopers.
Some of this variance is physical - there are Stormtroopers of varying heights (as can clearly be seen on the Death Star in A New Hope). These height differences, whether explained by less-pure cloning or non-clone recruitment, are visible and present throughout the movies. It's entirely likely that the Empire has a minimum height requirement for their recruited Stormtroopers. If so, it's possible that Luke is shorter than this. That said, physical height isn't the true cause for Leia's statements.
Leia, as a Senator, sees Stormtroopers a lot. As a Rebel leader, she's likely quite interested in their actions, limitations, and training. So when Luke walks in, it would be obvious to her that he's NOT a Stormtrooper. His armor is a close, but not perfect fit. His posture is all wrong (Stormtroopers stand tall, he hunches), and he wears his armor and carries his blaster rifle like someone who isn't used to either. So long as he was hurrying through the halls, following the lead of Solo (a well-travelled starpilot who a backwater farmboy would have admired) and intent on proving himself, Luke kept his awkwardness to a minimum. The second he entered the cell and saw the object of his quest (in an attractive 18-year old form) right in front of him? All that awkwardness and farmboy shyness came to the forefront.
Leia would have immediately known there was something different about this Stormtrooper. She was still trying to resist interrogation and spite Vader and Tarkin, and may have suspected this was a ploy by them. Her initial response was based off of that assumption: a derisive comment about the intruder's physical stature. Against someone sent to interrogate her, it would have failed. Against a farm boy who'd fallen into something so much bigger than himself, and who already was self-conscious? It had exactly the effect she was going for. Luke went on the defensive, trying to justify himself.
TL;DR: Luke is probably not below the minimum acceptable Stormtrooper height (the armor fits, after all) but showed many physical signs that indicated to Leia she could get an advantage over a potential adversary by making a derisive comment. "You're short" is the one she chose.
