The first thing to bear in mind is that the science class is not really intended to be a damage class. If you go in to it wanting to be anywhere but the lowest 1/3 on the damage chart, be prepared to be disappointed.
The primary purpose of sci is as crowd control, at which it is enormously effective, debuffing, or healing which it is also very good at.
That said, there are a few, very potent damage options.
First thing I will say is you almost have a very promising shield stripping build. Considering how much emphasis is placed on shield hardening, being able to completely negate them, can be very useful, and will help in your overall damage, and the damage of your team.
If you run Tachyon Beam 3 along with Charged Particle burst 3, you can strip over 9k shields in seconds. It can strip ALL shields clean off an escort, most off a cruiser, and a little less off a sci.
A few High Yield warheads on an unshielded escort will do some serious damage, so it works great with HY2. Very good if used with a partner with high burst DPS to take advantage of those moments.
I would recommend running 2x EPTS too for 100% uptime so your shields are permanently hardened.
Oh an don't waste valuable points on Polaron I use Tetryons on my shield stripper, otherwise I ALWAYS use disruptors or phasers. You get much more bang for your buck, giving you spare points to put in more useful areas.
This is a PvP space oriented build, so you will notice the lack of ground skills. If you intend to do any ground content, you might want to consider diverting some of the skill points where necessary. I will add that I don't have any problems with regular ground content. Battle Strategy and Combat Manoeuvres are also good skills to have specced, I'm not actually sure why I don't I will probably fix that shortly.
Eng: 7 aux power consoles, +35% Shield cap
Sci: 2x +18 Hazard systems 2x +16 Tractor Beam
Tac: 2x +26 Phaser weapons
Eng captain skills
This build is much tankier than the previous ones. The eng captain skills add a lot to your survival, there are also a few more heals floating about. I call this my "griefer" build, in that all its offensive sci skills are ones that can really annoy other people. I try to be the guy you really want to kill so he goes away, but hopefully can't.
Again this is a PvP space oriented build, so no ground skills, but the same applies. You will notice a wider spread of skills on this build, some that seem unrelated to my BOFF skills, this is to boost some of my captain skills. If I wanted to be extra annoying, I would stick a copy of scramble sensors in there too. But I'm kind
Both of these builds are very effective at what they do. Both carry TBR because it is so freaking fun It can also do a lot of damage. I have seen a max of ~15k straight to hull. The shield stripper will happily drain over 9k shields, more than most escorts have. HY1+2 to pound the hull, TBR to finish the job. The "griefer" will throw ships around the map like a baby having a tantrum.