It looks to me like Spectre equipment is (as it should be) the best of the best. However, I've only so far been able to find enough to fully equip Shepard and one other squad member. Is there a store that reliably stocks Spectre equipment? If so, how often does it get re-stocked?
Yes, Spectre gear can be acquired from vendors.
Once you unlock the "Rich" achievement/trophy by having 1 million credits on hand, the Alliance Requisition Officer (on the Normandy) and the C-Sec Requisition Officer (in C-Sec HQ) will offer Spectre weapons. If your character is level 50+ they will offer tier X (10) weapons, otherwise (level <= 49) they will offer tier VII (7) weapons. Spectre weapons, omni-tools, and amps exist at all 10 quality tiers, but only tier 7 & 10 weapons can be acquired without using the console commands.