I'm trying to work up some loads for my BCM SS410 upper and my Aimpoint with a 3x magnifier just isn't cutting it for shooting for groupings. I can't seem to reliably shoot better than about 2MOA with it, and sometimes worse. I'm looking for recommendations on an optic in the $200-$400 range, preferably the lower end. It will be used mostly at 100 yds and occasionally further. I'm thinking a basic 3-9 or 4-12 scope with a thin reticle might be ideal.

Leupold Rifleman is right inside your budget without mount.
 

Is there anything you can borrow from another rifle to do the quick work?  

If not, shot me an IM and I can get a loaner scope out to you.

However, if you plan to keep the optic and use it on that AR from time to time, I would suggest Midway's exclusive Grand Slam Tactical 3-10x40 and a Burris 1" QD PEPR mount.  Both will set you back $400.

I'd recommend at least 12x power. 16x would be better.  I had a good quality 3-9x and i was wanting more magnification when developing loads.

Really any cheap optic that holds a zero once mounted would do.  You dont need great glass or even matching turrets/reticle.  The only other thing Id look for is a thin reticle.  Maybe a Weaver Kaspa 4-16x for $150

I plan on using the scope for occasional long range shooting as well, but thank you for the offer.

How do you like that mount compared to other QD mounts such as Larue?

I would prefer an ADM or LaRue, as you can swap out ring size, but I tried to stay in your total budget.  However, there is nothing wrong with the Burris PEPR.

If you are going to use this optic on occasion, there is no need for a QD mount.