There are two ways to beat a Bohrok:
1) If it's multiple Bohroks at a time, then when they're about fire at you from there protected position, before they roll out of it double jump quickly and fire at them. Keep doing this and you'll win easily. However if you toa can use the Nuve special blast you could always use that.
2) When you're chasing a rolling Bohrok and knock it into the air, fire at it as quick as possible and you should beat it in no time.