i dont suggest that you use a cruiser as a science captain, just stick with a science ship or you will be blown to bits by a BoP. the cruiser will only give you more hull points and 2 more guns, but all those scoence abilities you will be losing will nerf your ability to do damage.
ENGs and SCIs can be put to work on almost every Ship if done right. So SCI and Cruiser can work. The only class that "has" to stick to the ship category is the poor tactical, and even here the others can preform better at times.
I have a science captain and I fly whatever I feel like (no real favorite available at tier 5), and cruisers still are not squishy even though I'm not an engineer, nor are my escorts (at least any more then you'd expect. You can fly what you want, just either spec yourself generally, and realize you won't have that extra hull and shield strength, or spec yourself into your ship of choice and fly whatever.
My KDF Science Captain uses Cruisers (Battlecruisers) and does okay with them. I honestly think the advice of "match the ship to the Captain" is an incorrect one, all three types of captain do fine with all three classes of ship. The difference is that each Captain approaches their ship from a different angle.
The thing to remember is that as a Science Captain, all you really have to distinguish yourself from other Captains are your Captain skills. You can get exactly the same BO layouts, with exactly the same weapons and devices. Maybe you can't train the same level III skills yourself, but that's minor. The main thing is, your ability to tank in your cruiser and to keep up your hull and shields are based in your BOs with EPtS, Reverse Shield Polarity, Engineering Team, Aux to SIF and so on.
What your Captain abilities give you are Sensor Scan, which is a great foe debuff, Dampening Field, which is a great self and ally buff, and Photonic Fleet, which draws damage off of you and deals a little addtional damage. (I think, I still haven't been able to quite tell if these ships are "real" or just decoys) In other words, you basically have two really good offensive and defensive abilities, which you can use to both do more damage to your foes (by scanning them before you shoot them) and protect yourself from damage. (By keeping your Dampening Field up as much as possible)
By contrast, a Tactical officer has better offensive buffs and debuffs, but lacks the ability to spread those buffs around as much to his team. The Engineering Officer has a great defensive buff for himself, with Rotate Shield Frequency, and has a lot of power management abilities (which works great with a broadsides Cruiser) but lacks offense. The Science officer has both offense and defense, and applies those bonuses to his team as well. So Science is more balanced, although it's more about active debuffs than passive bonuses.
In short, you might look for an opportunity to try to be a more offensive type of Cruiser captain, maybe using an Excelsior or a Sovereign, although you can also go with the Star Cruiser and have some good Science abilities you can stack with your own debuffs. Alternately, you can go with the DSSV or Nebula, and have a Science-type vessel which is more Cruiser-like. You might find that you like the Science ship abiliies. (Which have nothing to do with being a Science captain, they work for any captain in a Science ship)
I'll add that I didn't forget Subnucleonic Beam, I just don't find it as useful as the other Science powers. It is interesting to note, though, that Tactical captains get a power to speed up their OWN recharge, while Sci captains can slow down their OPPONENT'S recharge. There's kind of a resemblance there between Tac and Sci, as I said, Sci can be just as offensive, but is more team oriented, while Tac does a bit more damage, but isn't quite as good at absorbing the damage.
I play a UA science fed and i've never been on a science ship. I play both escorts and cruisers, never had a problem with them and i'm certainly not 'squishy'. I may not get a few of the extra skills when i level out some skills but the ones i do get make for a more versitle playing style.
I'll add that I didn't forget Subnucleonic Beam, I just don't find it as useful as the other Science powers.
I found that, at least in PvE, it's good for cancelling out that "methogentic" (or whatever it's called) sheild those minor races you encounter in the cluster explores (Vito'D, Scoodians, etc.) use on their cruisers. Just save your other buffs until you can cancel that ability, then unleash all heck on 'em.
As for a sci officer in a cruiser, I agree with the other posters: while a sci ship compliments a sci officer better, you shouldn't feel as if you're limited to a certain class of ship because of your career choice. My Gorn engineer pilots Varanus Fleet Support Vessel, which is a science ship (equivilent to the DSSV on the Fed side). It's just a matter of how you spec your skills.