In the end of Half-Blood Prince Harry explains to Ginny why they can't be together anymore:
"Voldemort uses people his enemies are close to. He's already used you as bait once, and that was just because you're my best friend's sister. Think how much danger you'll be in if we keep this up. He'll know, he'll find out. He'll try and get to me through you."
I assume this is referring to the time when Tom Riddle took Ginny into the Chamber of Secrets.
However, I don't see any indication that in that case he was using Ginny as bait because she was Harry's best friend's sister. He didn't have any control over who ended up with the diary. It happened to be Ginny because Lucius Malfoy chose to give it to her. If it had been Colin Creevey who had used the diary, Riddle would presumably have been unable to bring Ginny into the Chamber. He explains how he got her in:
"So I made Ginny write her own farewell on the wall and come down here to wait.
This makes it sound like he was able to force her to go into the Chamber because he was possessing her; had he been possessing someone else, though, he would not have been able to force Ginny to come.
Additionally, if Riddle could theoretically have forced anyone into the Chamber, then why would he use Ginny (who was only the sister of Harry's best friend) and not Ron (who was actually Harry's best friend? This again would seem to indicate that he used Ginny because that's who he had access to.
Furthermore, Riddle actually tells Harry what the primary bait was:
From everything Ginny had told me about you, I knew you would go to any lengths to solve the mystery – particularly if one of your best friends was attacked.
This seems to be referring to Hermione. Ginny would still have to be taken into the Chamber, but only in order for there to be a purpose for Harry to go there.
Also, while it is certainly possible that Ginny would have mentioned to Riddle that her brother was Harry's best friend, it's not actually mentioned anywhere that she told him this.
In light of the above, is there actually any evidence that Tom Riddle had targeted Ginny specifically because she was Harry's best friend's sister?