if I play whirlwind, can I choose an enemy's baron nashor?

Yes, you can choose an enemy Baron Nashor with Whirlwind.

According to RiftJudge FAQ #9057 and FAQ #3563, Whirlwind does not target or "choose" units; instead, it instructs players to make a choice during the spell's resolution.

Because Baron Nashor's ability states: "I can't be chosen by enemy spells and abilities," it specifically protects against spells that require the controller to target or choose the unit as part of the action. Since Whirlwind’s effect relies on the players making choices during resolution—rather than the spell itself targeting—the protection on Baron Nashor does not apply to this interaction.