Does commander tax apply when casting your commander from the command zone using alternative costs?

Commander tax (the additional {2} per previous cast from the command zone) is an additional cost, not part of the base mana cost. Per CR 903.8, each time you cast your commander from the command zone, you may pay an additional {2} for each time it was previously cast from the command zone this game. This applies regardless of how you are paying for the spell.

When you use an alternative cost (such as a free-cast effect like Omniscience, or a cost-reduction spell), you replace the base mana cost with the alternative cost. However, additional costs — including commander tax — are still applied on top of that alternative cost. CR 601.2b and CR 117.8 both confirm that alternative costs and additional costs are handled separately and both must be paid.

So if your commander has been cast twice before and you use Omniscience to cast it, you still owe {4} (the accumulated commander tax) even though Omniscience makes the base mana cost free. The alternative cost replaces the mana cost; it does not eliminate separately imposed additional costs.

Example: Your commander Atraxa has been cast from the command zone once before. You control Omniscience. When you cast Atraxa again, Omniscience makes her base mana cost {0}, but you must still pay the {2} commander tax, for a total of {2} to cast her.

The only way to avoid commander tax is to cast your commander from somewhere other than the command zone (e.g., your hand or graveyard, if it got there), since the tax only applies when casting from the command zone per CR 903.8.