The first to come to mind (and a personal favorite of mine as well) is Pistachio, which I know is quite popular in current-day Iran, and seems like it has quite a history in the region.
Also, I'm less sure on this, but I believe that Strawberry was used primarily medicinally up until the cross-breeding with a New-World variety and didn't really take off until the 18th century. IF so, that'd mean that the top 3 flavors of ice cream are quite new relative to its entire history. I'm really curious what the OG top flavors were across the centuries!
Step from the dusty street under a blazing Egyptian sun into the shade of an artisan family's house in the high Middle Ages, and you might indeed look forward to a tasty frosty snack. But set aside thoughts of "ice cream" in the sense of twist soft-serve. When Pietro della Valle and John Fryer traveled to Persia in the 17th century, they described treats of literal-ice (or snow) cold "water, wine, and sherbets." We're talking more about slushies, snow-cones, or even chillers/sherbats than an Oreo concrete.
So aside from the occasional (okay, one that I know of: "wine shall...freeze, that you cannot drink it but by sucking") reference to people making wine popsicles, a medieval or early modern sherbet that aimed a step higher than ice in a liquid would most likely be fruit flavored. Fryer, in fact, explicitly attributes the sale of sherbets to fruit-sellers, naming plums, pomegranates, and limes as the usual suspects for flavors.
Far more fun for present purposes, though, and the reason I referred to Cairo above, is the (probably) tenth-century cookbook attributed to Ibn Sayyar al-Warraq. Al-Warraq gives several recipes for thicky, syrupy fruit drinks that scholars have considered the equivalent of sherbets and sherbats.
A recipe for pomegranate drink:
Cook well together 9 parts pomegranate juice and 1 part honey. Stir into the liquid cooked grape wine made by boiling it down to a third of its original amount. Shake the drink and empty it into a clean vessel. You may flavor it with a bit of spices.
A recipe for plum drink with honey:
Take as much as you like of unripe plums, remove the pits, pound them, and press out their juice. Take one part of this juice and one part honey, which has been [boiled and] skimmed of its froth. Cook them together under a slow fire until mix develops a thick consistency. You have the option of replacing honey with white cane sugar.
Some of al-Warraq's recipes are a bit more elaborate and specific:
Drink of unripe grapes
Take 10 parts juice of unripe grapes and 3 parts honey. Put them in a clean pot. Take saffron, spikenard, Ceylon cinnamon, cassia, white mastic gum, and camphor, a bit of each. Grind them and add them to the pot. Let the pot boil twice or thrice.4 Then, take the fire away from underneath the pot to let the drink cool down. Empty the drink into vessels and use it as needed, God willing.
("God willing" is a standard formula, of course, but one wonders if it was particularly heartfelt on occasions such as this.)
At least in the text, there is an additional factor in play. Al-Warraq argues for the medicinal value of the syrup surrounding the ice. Hence the requirement of specific spices in the grape syrup drink, which, working within the theory of the humors, he intends explictly intends will combat an excess of yellow bile. Buried in this is the implicit, self-evident principle that sherbet itself is beneficial for the human body.
The idea of fruit, unsurprisingly, made it back to Italy to help ground Europe's first infatuation with sorbetti. It wasn't alone, though. Chocolate and cinnamon were also crucial early flavors. (Although we think of vanilla as the default and/or flavor-neutral, actual vanilla was far too expensive and rare to use.) Along with OP's recognition of cocoa as a western hemisphere plant, you might pick up on cinnamon as exotic from the other direction. Although Melissa Calaresu has done really cool work to show that ice cream in the 1700s was the food of the people, not just the elite, it was still very associated with prestige and high society (when served in the most elaborate and expensive dishes, of course). So it's not surprisingly that the luxury of ice would meet the luxury of chocolate.
If you’re now interested how Vanilla became the standard ice cream flavour, you can read this answer from u/fisch09