When bomb tokens trigger, can you choose a new target each deathknell?

Yes — each Bomb is a separate permanent with its own Deathknell instance, so each one adds its own trigger to the chain and each picks its own target when it finalizes (Rule 808.2). If three Bombs die at once, you make three independent "deal 2 to an enemy unit here" choices — they can be three different enemies, or the same one three times.

Two limits. The choice is locked at finalization, not resolution (Rule 355.5.b), so you can't wait to see the first trigger's damage land and then redirect the second. And "here" is noted from where that Bomb was before it hit the trash (Rule 808.1.d.3), so each trigger only reaches enemies at its own Bomb's battlefield — Bombs that died at a different location can't help each other. If a target gets killed by an earlier trigger in the stack or by a Reaction, the later trigger simply mistargets and its 2 damage does nothing — though its "kill your other Bombs here" still happens, since that part isn't a choice.