Thinking of changing my weaponry so can someone tell em what they think the best beam weapons are for a science captain as well as the best torpedos. I currently use
Fore: 3 Phased Tetryon Beams and a Quantum Torpedo (Borg)
Aft: 3 Phased Tetryon Beams with a Tricobalt Torpedo launcher

Phased tetryon for shield drain and subsystem knockout
Phased polaron for shield drain and subsystem drain
Spiral wave disruptor (very hard to get) for DPS and subsystem knockout
Polarised disruptor for DPS and subsystem drain.

Shield drain is kind of useless because its only a few hundred shield damage that becomes useless quickly in PvE and doesn't act fast enough to dent in PvP.
Polaron subsystem drain effects more sub systems. While you won't knock weapons offline, you can have them at far below their regular strength while often causing significant drain to shields, engines, and auxillary (depending on which your enemy neglects).

My favorite at the moment is the Polarised disruptor but thats only because I haven't lucked into a Galor to loot for weapons yet.

For torpedoes, you could try out the Hargh'Peng. Slightly stronger than Quantums with a lasting Hargh'Peng radiation that has a better DoT than plasma followed by an explosion that damages your enemy behind their shields.

What kind of ship you're flying? What kind of BOFFs have you got?

It seems to me that you're mixing too many energy types! Also You don't know what kind of Ship he's flying. My SCI Character is flying a Luna class...but I cannot have the same SCI playstyle that I enjoy when I switch to my Atrox Carrier (with the same SCI Character, of course).

he is not mixing anything. he is suggesting sepperate energy types for sepperate things.
he is only telling which does what best.
In no word did he suggest mixing them. Although some actually can be mixed.

for instance a spiral wave disruptor and a polarised disruptor profit both from disruptor consoles as far as i know.
and polarons and tetryons proc profit from the flow capacitator skill a little bit. Also certain ships/sets boost certain dmg types.

nothing worng with the beams you have...phased tetryons are good...there is no "best" energy types...but some are certainly better than others. But mostly they are situational or can be tuned towards a certain skillset.

I use a Mirror Universe Star Cruiser I perform well in both STF's and fleet actions and was just think about changing my weaponry slightly and wondered if there was better ones than the Phased tetryons since there is nothing really better I think I will just keep it the way it is

Outside of PvP it barely matters what energy type you use. You should generally use the type for which you have the best associated tac and sci consoles, as they are the most expensive part. Seems to me that AP (presumably fleet) are most popular, along with phased tetryons and a few of the other double-procs.