Can attacking players use activated abilities after blockers have been declared?

Yes, attacking players can activate abilities after blockers have been declared, but before damage is dealt, to modify the amount of damage that will be dealt. (See Glorfindel's answer for complete rules on this).

However, in your particular case, it seems that there is some miscommunication that occurred in your game; where someone acted out of turn, and it's not clear whether that was you or your opponent.

Once blockers are declared, both players get a chance to activate abilities or cast instants. When the stack is cleared and both players pass priority, combat damage is then dealt simultaneously:

510. Combat Damage Step

510.1. First, the active player announces how each attacking creature assigns its combat damage, then the defending player announces how each blocking creature assigns its combat damage. This turn-based action doesn’t use the stack. A player assigns a creature’s combat damage according to the following rules:

510.2. Second, all combat damage that’s been assigned is dealt simultaneously. This turn-based action doesn’t use the stack. No player has the chance to cast spells or activate abilities between the time combat damage is assigned and the time it’s dealt.

After you declared blockers, you say you moved your commander to the command zone. But it isn't clear if you only did this after both you and your opponent said that you were passing priority. If you simply said "I'm blocking with Anafenza", and then moved Anafenza to the Command Zone, then you acted out of turn, because it was not yet time for combat damage to be dealt.

You also did not say if your opponent expected Yasova to die or not. If your opponent did not activate Bow of Nylea until after combat damage were dealt (which he would be doing in the end of combat step), then Yasova would die due to having 4 damage and 4 toughness. But if your opponent was activating Bow of Nylea during the declare blockers step, before combat damage was dealt, then Yasova would still be alive, having 4 damage and 5 toughness.

So the correct answer comes down to the communication that took place after you declared your blockers. Did your opponent make an indication that he was ready for combat damage to be dealt? Or did you just assume that as soon as the blockers were assigned, combat damage was happening? Aside from the 1 difference in how much damage you would take, it would also determine whether or not your opponent's commander lived or died.

506. Combat Phase

506.1. The combat phase has five steps, which proceed in order: beginning of combat, declare attackers, declare blockers, combat damage, and end of combat. The declare blockers and combat damage steps are skipped if no creatures are declared as attackers or put onto the battlefield attacking (see rule 508.8). There are two combat damage steps if any attacking or blocking creature has first strike (see rule 702.7) or double strike (see rule 702.4).

509. Declare Blockers Step

509.4. Fourth, the active player gets priority. (See rule 116, “Timing and Priority.”)

So there is room (for either player) to cast spells or activate abilities after blockers have been declared and before combat damage is being assigned.

But what you describe, "moving her to the command zone" looks like combat damage has already been assigned and dealt. Your opponent can still pump up their creature (in the general case; it looks like it should've already died, as @Arthur noted in the comments), but it won't affect the combat damage already dealt.