I am always ready with a subnuke when I am tractoring or using gravity well, in pvp at least, it's so funny.

Polarize hull is hard counter to tractor beams. Warbird probably viral matrix you, and your auxiliary power went down, hence your polarize hull disappears. Remember most of the science skills (including polarize hull) is auxiliary dependent, one way or another. Soft counter to tractor beams is Attack pattern Omega, which has issues with it, especially if u are hold with multiple tractor beams.

PH does have some issues against tractors, it gives off an immune to each tractor pulse. Sometimes that immunity lags making you stop, if you are lagging PH doesn't work at all.

Really it ought to be the other way around. Polarizing the hull throws science at the problem and provides a REASON for tractor beams to not affect you. Pattern Omega affecting tractor beam lock is some kind of "mind over matter" weirdness. If your conn officer thinks hard enough, tractors stop affecting you? No. That's stupid.

Another really hard counter (but more likely situational) to tractor beams is Photonic Shockwave. The shockwave's disable interrupts abilities that have wind-up or tick-over-time, such as the (assimilated) tractor beam, tachyon beam, and Donatra's Biogenic Charge attack.
I haven't had enough experience to see what other abilities it interrupts, as I'm sure there are more things it can hamper. Still, even when an escort is shut down for a couple of seconds due to the shockwave is reason enough to use it.

The HUGE downsides are that it has a 3km radius, meaning you have to push towards the beamer, and that it requires a minimum of a Lt-Com Sci slot

Another counter is photonic torpedo, something I have seen fed NPCs use on an annoyingly regular basis, especially when they get tractored/I am beating the living snot out of them. Oddly enough, I only see it on NPC science ships, and I never see players using it, so this is possibly a moot point since it's possibly an NPC only item.

They come with the Long Range Science Vessel Refit (Bellerophon class).

I stand corrected. Why don't you see more of them in use then? I know that the Intrepid class NPCs aren't the only ones using them on me, more often than not it's actually the Polaris class NPCs that do it.

All the Federation Science Vessels use it. That includes the standard ones (Polaris, Luna, Destiny, etc), the Intrepid, the Nebula, and the Rhode Island.

Repulsors are a good bet