BOH-KOH-BLIHN, like cocoa.
While that was my first assumption on how to pronounce it, it also always made the most sense to me, considering what the term "boko" actually was in the game the term first appeared in (The Wind Waker), which was merely an enemy name prefix. We forget this now because Bokoblins are a staple enemy now and the only one with the prefix that originated in TWW that I can recall, but there were others, like the Boko Baba. People refer to the "blin" suffix as if it's supposed to refer to goblins, which as I understand is why people think it's pronounced like "goblin", but pronouncing "boko" in that way in the Boko Baba name would sound bad. xP Same with Boko Sticks, etc.