I think that Pulsars are currently the strongest guns.

Why Alchemers are bad

Alchemers fail of how they can't handle single target foes very well, with the exception of its charge, which is more powerful and deals obnoxious status effects. If I want to alchemer 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.

Alchemers are also especially prone to sword hell- you have to get in to charge your Alchemers, and you cannot shield at all while charging. While doable, this still introduces extra strain on the player. Why bother Alchemering when you can just fall back and Pulsar down the opposition?

Why All Other Guns Are Bad

A lot of people are quick to point out that Pulsars have lower damage than stronger guns. 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 valiancer I am, I'll always have to have greater risk when attacking faster than I would from further with a Pulsar.

Further, the majority of strategies I've seen used to defeat the harder content in Spiral Knights revolve around Pulsars, because most of the harder enemies punish you for using other handguns. They do this by shooting slow projectiles at you, laying traps down, launching rockets at you, unleashing their ultimate attacks which are very difficult to deal with other guns. All of these scenarios make it very likely that you'll take damage using an other handgun against whatever you're fighting.

Why Pulsars Are Good

Pulsars 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 obnoxious and not-so-efficient statuses that allow you to clump together and not-really stall mobs for lengths of time as well as snipe them. If I'm using Nova Driver or Storm Driver, I have to risk not dealing status effects, and I'm screwed by other enemies. If I'm using Pulsar, I can deal very similar damage from quite far off with a well aimed explosion, or I can strafe and fire off regular shots while dodging.

The same goes for valiance. If I fire from a distance, I only deal area a narrow scope of damage at a distance, but like all handguns, a bit more safely. If I tried to knock them to the corner, there would not be enough knockback to do that. Valiance have fairly moderate single target damage as well. A full party of people using this tactic will not work out.

Blitz needle offers random damage of all kinds from a distance. It immobilizes the user, which is a huge drawback and makes it really not all that amazing. When that happens, you're frozen. It also helps out when you know what you're doing worse than you have any right to. I can kill 3 slags in a flurry of pulsar bullets after freezing them in place correctly. Pulsars have more significance, but I'll get to that later.

Argent peacemaker have much less crowd control, and offer the slow-walking risk that I feel they are certainly worth mentioning. If you fire 6 shots from Argent peacemaker, you are very slow, AND are at a much greater risk than shooting 3 bullets from a pulsar. Having more than 2 shots that don't deal area damage gives these Argent Peacemakers huge disadvantage that Pulsars luckily do not have. You can almost just throw away your Argent Peacemaker because Pulsar is overall much better in all scenarios.

The biggest counter to Pulsars 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 Pulsar spam. Most healing mobs rely on a mender of some sort, which can also be shut down using a Supernova (because elemental pulsars will not be as effective). Those with respawning healers can be dealt with using elemental pulsars, to fully maximize damage with status effects taken.