I think that guns are currently the strongest weapon type.
Why bombs are bad
Bombs fail because of how they can't handle single target foes very well, with the exception of dark retribution, which is but one bomb limited to shadow damage. If I want to bomb vanaduke, my damage is going down the drain because vanaduke isn't 20 mobs, he's one mob with one health bar that takes forever to reduce. The same goes for tortodrones and every other large mob.
Bombs are also especially prone to bullet hell- you have to get in to drop your bomb, and you cannot shield at all while charging. While doable, this still introduces extra strain on the player. Why bother bombing when you can just fall back and gun down the opposition?
Why swords are bad
A lot of people are quick to point out that handguns have lower damage than swords. But I like to point out that the game doesn't care how high your damage per second is, it cares how high your damage per second per damage taken is. No matter how good a swordy I am, I'll always have to have greater risk when attacking up close than I would from further with a handgun.
Further, the majority of strategies I've seen used to defeat the harder content in Spiral Knights revolve around handguns, because most of the harder enemies punish you for using swords. They do this by dealing area damage from up close, dropping poisonous splotches, surrounding themselves with fire balls, and using bullet hell against you. All of these scenarios make it very likely that you'll take damage using a sword against whatever you're fighting.
Why handguns are good
Handguns have area control at a distance as well as high single target damage, also at a distance. This combination is typically what you should be shooting for. (That pun.)
The alchemers deal heavy statuses that allow you to clump together and stall mobs for lengths of time as well as snipe them. If I'm using acheron or combuster, I have to walk up to a turret to hit it. If I'm using nova driver, I can deal very similar damage from quite far off with a well aimed charge attack, or I can strafe and fire off regular shots while dodging.
The same goes for pulsars. If I fire from a distance, I deal area damage at a distance, safely. If I knock them into a corner or immobilize them, I have fairly high single target damage as well. A full party of people using this tactic works particularly well with itself.
Blitz needle offers high damage of all kinds from a distance. It immobilizes the user, which is a huge drawback and makes it really not all that amazing, except for against slow, frozen, or shielded mobs. When that happens, you're golden. It also helps out when you know what you're doing better than you have any right to. I can kill 3 slags in one charge after freezing them in place correctly. It has more significance, but I'll get to that later.
Carbine, valiance and argent peacemaker have less crowd control, but offer such great safety that I feel they are certainly worth mentioning. Having more than 2 shots that don't deal area damage gives them huge utility that swords and bombs lack almost completely-- especially for carbine/argent. You can almost just forgo all notion of being the most damaging awesome thing and survive indefinitely to win.
The biggest counter to handguns are also defeated best by them. Almirian crusaders and mecha knights can be dealt with easily by manipulating their shield tactics, while trojans and other large shielded mobs are notably defeated by autoguns. Most healing mobs rely on a mender of some sort, which can also be shut down using a handgun.. those with respawning healers can be dealt with using autoguns, to fully maximize damage taken.
I would like to challenge this by saying that guns are not simply the outright best - as with absolutely every weapon in this game, it depends on what situation you're in. I hate using such a dull argument, but it's dull because everyone says it, and everyone says it because it's true.
For example, in almost every situation bar bullethell and single targets, a nitronome will murder everything in the game with fairly low risk, similar to the safety that you claim guns provide. Simply inturrupt and knockback everything until it's dead. Add enough damage boost for turret flinching and even a lot of bullethell scenarios are a lot easier.
I am eager to be corrected.