Each at their best. When Shino was first introduced he was my favorite before he went from a badass mysterious bug user to "I just want friends". Both Shino and Shikamaru are the smartest of the Konoha 11 and they always win by thinking steps ahead of their opponents. The Aburame clan is one of the 4 noble clans of Konoha and Shino showed enough potential at a young age for Danzo to try to recruit him. Shikamaru was the first to become Chunnin but Shino never got the chance to show his skills, I think he would have become Chunnin along with Shikamaru. Although we don't know much about their current skills since the one time we see Shino fighting he was being controlled so that was not his best. Shikamaru seems to have improved a lot since Shippuden but we haven't seen much. I'll give the victory to Shino 7 out of 10 since the Aburame bugs seem much more versatile than the Nara Shadows.
If we're talking about their Boruto counterparts, then victory certainly goes to Shikamaru. He's a jonin, and Shino is still a chunin (and he's certainly not a victim of situation like Naruto and Sasuke were). Even if we didn't consider ranks, Shikamaru's genius has been shown to be able to overcome vastly superior firepower and ability. Shino is strong but it's likely he's still a chunin because he's capped out.