If I kill a bomb token with the additional cost of playing Shimmering Swimmer, would the bombs deathknell and the Swimmer's when played trigger go on the chain simultaneously?

Yes — if you kill your own Bomb token as the additional cost for Shimmering Swimmer, the Bomb's Deathknell and the Swimmer's "when you play me" trigger are placed on the chain simultaneously, and since you control both you choose the order they go on (Rule 383.3.d; FAQ #6068). The Swimmer resolves fully and enters play first, then both triggers are queued together — that's the standard "additional cost kills a friendly permanent" timing.

The Bomb is a gear token, but tokens can have and trigger Deathknell just fine (Rule 808.1.d), so nothing there changes. Note the Bomb's ability is not optional and not friendly: it deals 2 to an enemy unit "here" and kills your other Bombs at that location — "here" is locked in at the Bomb's old location, where the Swimmer isn't (it enters at your Base or a battlefield you control). The Swimmer's half deals 2 to a unit of your choice, so it can hit that same enemy unit or anything else.

Whichever went on the chain last resolves first; if you want the Swimmer's 2 damage to finish off a unit the Bomb also damaged, order accordingly.