Hmm, I think the only ships that would let you have both Eject Warp Plasma and Gravity Well are the Magellan and Odyssey, though you can do just fine with an RSV or DSSV, depending what ensign you want. Nothing else lets you have LtCmdr Engineer and Sci together.
Between the two, I prefer Gravity Well, as it lets you activate your main CC at range instead of having to get close enough to 'crop dust,' particularly when doing so with the speed of a cruiser. Also be sure to slot a good Gravimetric Scientist for the chance for one GW to spawn others, and a Tractor Beam Officer so your hold also drains shields. And of course I know some people swear by Tyken's Rift for debuffing, but that isn't as strictly CC as GW is.
As for weapons you'll probably want either (phased) polaron or (polarized) tetryon. If you're doing CC you're likely part of a team I'm guessing, and as a science ship you won't have the firepower to be the heavy hitter. On the other hand shield-stripping makes a good complimentary ability to CC, hence weapons with power and shield drain. And there's always the Tetryon Glider from the Omega set, if you have the EDC resources to go all-in that way, plus a complete set gives you the Gravitic Anchor as well.
Just out of curiosity, are you meaning a PC or a BOFF? If a player captain, run, flee, do not look back. Science is about to get beaten to death by the nerf stick, so that DPS can do better. If you mean a Boff it is dependent, I don't trust/use my crew as anything more than dps/support. Also it depends on play style and your own class. I've run a 4 tac grenade crew with a sci officer for heals a 3 engie turret of doom crew with 2 science for support/heals/debuff and a 2/2/1 set up as well. All of them are fun in different ways, all of them can be a blast, but all of them can get plastered at times as well. My suggestion, get as many white common boffs as you can and play around with them, as you learn you will then figure out what you want to do and how you want to play. BOFF's can be a bit hard to learn but you can do so many fun combo's it does make it worth it.
Here are the abilities that might be useful on a BOFF for crowd control:
Electro-Gravitic Field: Produces an AoE Root or Slow centered on the target
Anesthizene Gas: Produces an AoE Slow and Damage debuff centered on the target, 50% chance of brief Stun
Stasis Field: Produces an AoE fragile Hold centered on the target
Neural Neutralizer: Produces an AoE Placate centered on the character using it
Sonic Pulse: Produces an AoE Knockback, Interrupt, and moderate damage centered on the character using it
Hyperonic Radiation: Produces an AoE damage-over-time effect centered on the target.
A Science Captain also has access to:
Dampening Field: Produces an AoE Damage debuff centered on the target
Exothermic Induction Field: Produces a powerful AoE damage-over-time effect centered on the target. This ability is strong enough to one-shot weaker NPCs if you have the Mk X level kit and have at least three levels in the kit-boosting ground skill. Think of it as the Science equivalent to Orbital Strike, and you won't be far off.
Just out of curiosity, are you meaning a PC or a BOFF? .
I have a lvl 50 of each class, and for each I run with 2 sci and 2 eng. Both engineers have shield repair I and levels I,II and III of turrets
1 science has med triquarder I,II and III and vascular regen III
the other sciences have diff skills on each character cause I've been trying to test some of the crowd control skills. This character feels like a wasted spot on every single roster. never seems to have much of an impact. I don't notice much stunning or holding going on no matter the skills