Wow. Just got ninja'd by 7 posts... well here goes nothing.
I don't think gunners are useless right now. They provide diversity to the weapons on your ship. They help change variables in battle that were previously taking you down.
That being said, there is a certain imbalance, but I think it's actually the engineer that is the problem.
The way the tools are set up is that any class (gunner, engi, pilot) can perform any role (gunning, repairing, flying) with the right tools. The number of tools your class allows, increases your performance at that role (which makes the Spyglass the odd one out and why I think there should be a Gneral tool slot...).
But what it comes down to is, engis and gunners take the Spyglass for the Pilot tool, and most gunners take Pipe Wrench for repair because they're not going to be able to use anything else.
The Engineer still has that versatility of having all of the ammo types be useful for whatever guns they're ship has.