I just lowered my 00 honda civic si and went to get an alignment and found out that they could not do it because of the oem lower conrtol arm's. I was wondering what controls arms would fix this problem and which ones would be the best.

 

If your LCA's are stock then they told you wrong, whether fronts or rears. Toe shouldn't be affected by lowering. It's camber. Some shops are asses and won't align a lowered car. What I'd do is call around and find one that will do an alignment. Usually they will just give you a disclaimer about aligning your car as close to factory specs as possible.
If more than 1.75 inch drop, it would be in your best interest to install front and rear camber kits.
Good luck.